Soybean variety 5PYPS54

ABSTRACT

A novel soybean variety, designated 5PYPS54 is provided. Also provided are the seeds of soybean variety 5PYPS54, cells from soybean variety 5PYPS54, plants of soybean 5PYPS54, and plant parts of soybean variety 5PYPS54. Methods provided include producing a soybean plant by crossing soybean variety 5PYPS54 with another soybean plant, methods for introgressing a transgenic trait, a mutant trait, and/or a native trait into soybean variety 5PYPS54, methods for producing other soybean varieties or plant parts derived from soybean variety 5PYPS54, and methods of characterizing soybean variety 5PYPS54. Soybean seed, cells, plants, germplasm, breeding lines, varieties, and plant parts produced by these methods and/or derived from soybean variety 5PYPS54 are further provided.

BACKGROUND

There are numerous steps in the development of any novel, desirablesoybean variety. Plant breeding begins with the analysis and definitionof problems and weaknesses of the current germplasm, the establishmentof program goals, and the definition of specific breeding objectives.The next step is selection of germplasm that possess the traits to meetthe program goals. The breeder's goal is to combine in a single varietyan improved combination of desirable traits. These traits may includehigher seed yield, resistance to diseases and insects, reducing the timeto crop maturity, tolerance to drought and/or heat, altered fatty acidprofiles, abiotic stress tolerance, improvements in compositionaltraits, and better agronomic characteristics.

These product development processes, which lead to the final step ofmarketing and distribution, can take from six to twelve years from thetime the first cross is made until the finished seed is delivered to thefarmer for planting. Therefore, development of new varieties is atime-consuming process that requires precise planning, efficient use ofresources, and a minimum of changes in direction.

A continuing goal of soybean breeders is to develop stable, highyielding soybean varieties that are agronomically sound with maximalyield over one or more different conditions and environments.

SUMMARY

A novel soybean variety, designated 5PYPS54 is provided. Also providedare the seeds of soybean variety 5PYPS54, cells from soybean variety5PYPS54, plants of soybean 5PYPS54, and plant parts of soybean variety5PYPS54. Methods provided include producing a soybean plant by crossingsoybean variety 5PYPS54 with another soybean plant, methods forintrogressing a transgenic trait, a mutant trait, and/or a native traitinto soybean variety 5PYPS54, methods for producing other soybeanvarieties or plant parts derived from soybean variety 5PYPS54, andmethods of characterizing soybean variety 5PYPS54. Soybean seed, cells,plants, germplasm, breeding lines, varieties, and plant parts producedby these methods and/or derived from soybean variety 5PYPS54 are furtherprovided.

DETAILED DESCRIPTION Definitions

Certain definitions used in the specification are provided below. Also,in the examples and tables which follow, a number of terms are used. Inorder to provide a clear and consistent understanding of thespecification and claims, the following definitions are provided:

AERBLT=AWB=AERIAL WEB BLIGHT. Aerial web blight is caused by the fungusRhizoctonia solani, which can also cause seedling blight and root rot ofsoybeans. Stems, flowers, pods, petioles, and leaves are susceptible toformation of lesions. Tolerance to Aerial Web Blight is rated on a scaleof 1 to 9, relative to known checks, with a score of 1 beingsusceptible, and a score of 9 being tolerant. Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

ALLELE. Any of one or more alternative forms of a genetic sequence. In adiploid cell or organism, the two alleles of a given sequence typicallyoccupy corresponding loci on a pair of homologous chromosomes.

ANTHESIS. The time of a flower's opening.

ANTHRACNOSE. Anthracnose is a fungal disease commonly caused byColletotrichum truncatum, and in some cases other Colletotrichum speciesmay be involved. The fungus produces crowded, black acervuli on infectedtissues. These dark bodies typically look like pin cushions on thetissue surface when viewed under magnification. The most common symptomsare brown, irregularly shaped spots on stem, pods and petioles.Resistance is visually scored on a range from 1 to 9 comparing allgenotypes in a given experiment. A score of 9 indicates that there is noinfection (resistance). Preliminary scores are reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

APHID ANTIBIOSIS. Aphid antibiosis is the ability of a variety to reducethe survival, growth, or reproduction of aphids that feed on it.Screening scores are based on the ability of the plant to decrease therate of aphid reproduction. Plants are compared to resistant andsusceptible check plants grown in the same experiment. Scores of1=susceptible, 3=below average, 5=average, 7=above average, and9=exceptional tolerance. Preliminary scores are reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

APHID ANTIXENOSIS. Aphid antixenosis is a property of a variety toreduce the feeding of aphids upon the plant, this is also known asnonpreference. Screening scores are based on the ability of the plant todecrease the rate of aphid reproduction. Plants are compared toresistant and susceptible check plants grown in the same experiment.Scores of 1=susceptible plants covered with aphids, plants may showsevere damage such as stunting and/or necrosis, equivalent or worse whencompared to susceptible check, 3=below average, plants show major damagesuch as stunting and/or foliar necrosis, 5=moderately susceptible,7=above average, about 50 aphids on the plant, plant does not exhibitsigns of plant stress, and 9=exceptional tolerance, very few aphids onthe plant, equivalent or better when compared to a resistant check.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

BACKCROSSING. Process in which a breeder crosses a donor parent varietypossessing a desired trait or traits to a recurrent parent variety(which is agronomically superior but lacks the desired level or presenceof one or more traits) and then crosses the resultant progeny back tothe recurrent parent one or more times. Backcrossing can be used tointroduce one or more desired traits from one genetic background intoanother background that is lacking the desired traits.

BLUP=BEST LINEAR UNBIASED PREDICTION. The BLUP values are determinedfrom a mixed model analysis of variety performance observations atvarious locations and replications.

BREEDING. The genetic manipulation of living organisms, includingapplication of one or more agricultural and/or biotechnological tools,methods and/or processes to create useful new distinct varieties.

BU/A=Bushels per Acre. The seed yield in bushels/acre is the actualyield of the grain at harvest.

BROWN STEM ROT=BSR=Brown Stem Rot Tolerance. This is a visual diseasescore from 1 to 9 comparing all genotypes in a given test. The score isbased on symptoms on leaves and/or stems such as yellowing, necrosis,and on inner stem rotting caused by Phialophora gregata. A score of 1indicates severe symptoms of leaf yellowing and necrosis. Increasingvisual scores from 2 to 8 indicate additional levels of tolerance, whilea score of 9 indicates no symptoms. Preliminary scores are reported asdouble digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

BSRLF=Brown Stem Rot disease rating based solely on leaf diseasesymptoms. This is a visual disease score from 1 to 9 comparing allgenotypes in a given test. A score of 1 indicates severe leaf yellowingand necrosis. Increasing visual scores from 2 to 8 indicate additionallevels of tolerance, while a score of 9 indicates no leaf symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

BSRSTM=Brown Stem Rot disease rating based solely on stem diseasesymptoms. This is a visual disease score from 1 to 9 comparing allgenotypes in a given test. A score of 1 indicates severe necrosis on theinner stem tissues. Increasing visual scores from 2 to 8 indicateadditional levels of tolerance, while a score of 9 indicates no innerstem symptoms. Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

CELL. Cell as used herein includes a plant cell, whether isolated, intissue culture, or incorporated in a plant or plant part. The cell canbe a cell, such as a somatic cell, of the variety having the same set ofchromosomes as the cells of the deposited seed, or, if the cell containsa locus conversion or transgene, otherwise having the same oressentially the same set of chromosomes as the cells of the depositedseed.

CERK=CERCOSPORA TOLERANCE=Cercospora field. A fungal disease caused byCercospora kukuchii which can be identified by symptoms including one ormore of mottled reddish-purple discoloration of the uppermost leaves ofthe soybean plant, mottled discoloration of leaf petioles, mottleddiscoloration of pods, and/or purple discoloration of the seed coat.Infected seed, having a purple discoloration, is commonly referred to aspurple seed stain. For the multiple expressions of this disease, plantsor plant parts are visually scored from 1 to 9 relative to picturediagrams for each trait. A score of 1 indicates severe symptoms, while ascore of 9 indicates no visual symptoms. Preliminary scores are reportedas double digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

CRDC=CHARCOAL ROT DROUGHT COMPLEX=Charcoal Rot. A fungal disease causedby Macrophomina phaseolina that is enhanced by hot and dry conditions,especially during reproductive growth stages. Tolerance score is basedon field observations of the comparative ability to tolerate drought andlimit losses from charcoal rot infection among various soybeanvarieties. A score of 1 indicates severe charcoal rot on the roots anddark microsclerotia on the lower stem causing significant plant death.Increasing visual scores from 2 to 8 indicate additional levels oftolerance, while a score of 9 indicates no lower stem and/or root rotand no visual symptoms. Preliminary scores are reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

CHLORIDE SALT TOLERANCE=Chloride sensitivity. This is a measure of thechloride salt concentration in seedling plant tissue, arrayed on a scalebased on checks, and scores applied from 1 to 9. The higher the scorethe lower the concentration of chloride salts in the tissue measured.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

CW=Canopy Width. This is a visual observation of the canopy width whichis scored from 1 to 9 comparing all genotypes in a given test. A scoreof 1=very narrow, while a score of 9=very bushy. Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

CNKST=SOUTHERN STEM CANKER TOLERANCE. This is a visual disease scorefrom 1 to 9 comparing genotypes to standard checks chosen to arraydifferences. The score is based upon field reaction to the disease. Thecausative agent is Diaporthe phaseolorum var. meridionalis (SouthernStem Canker), which tends to impact southern geographic regions. A scoreof 1 indicates susceptibility to the disease, whereas a score of 9indicates the line is resistant to the disease. Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

CNKSG=SOUTHERN STEM CANKER GENETIC. This is a visual disease score from1 to 9 comparing genotypes to standard checks chosen to arraydifferences. The score is based upon toothpick bioassay in (1) field orshade tent bioassays or (2) controlled environmental chambers, and isbased on genetics that infers resistance or susceptibility to SouthernStem Canker. Diaporthe phaseollorum var. meridionalis is the causativeagent. A score of 1 indicates severe stem canker lesions, relative toknown susceptible check varieties, whereas a score of 9 indicates nomeaningful disease symptoms, consistent with known resistant checkvarieties. Preliminary scores are reported as double digits, for example‘99’ indicates a preliminary score of 9 on the scale of 1 to 9.

COTYLEDON. A cotyledon is a type of seed leaf. The cotyledon containsthe food storage tissues of the seed.

CROSS-POLLINATION. Fertilization by the union of two gametes fromdifferent plants.

DIPLOID. A cell or organism having two sets of chromosomes.

DM=DOWNY MILDEW. A fungal disease caused by Peronospora manshurica insoybean. Symptoms first appear on leaves, which can spread to podswithout obvious external symptoms, and further spread to seed. Infectedseed may have a dull white appearance. The tolerance score is based onobservations of symptoms on the leaves of plants regarding leaf damageand/or level of infection. On a scale of 1 to 9, a score of 1 indicatessevere symptoms, whereas a score of 9 indicates no disease symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

ELITE VARIETY. A variety that is sufficiently homozygous and homogeneousto be used for commercial grain production. An elite variety may also beused in further breeding.

EMBRYO. The embryo is the small plant contained within a mature seed.

EMGSC=Emergence Score=Field Emergence. A score based upon speed andstrength of emergence at sub-optimal conditions. Rating is done at theunifoliate to first trifoliate stages of growth. A score using a 1 to 9scale is given, with 1 being the poorest and 9 the best. Scores of 1, 2,and 3=degrees of unacceptable stands; slow growth and poor plant health.Scores of 4, 5, 6=degrees of less than optimal stands; moderate growthand plant health. Scores of 7, 8, 9=degrees of optimal stands; vigorousgrowth and plant health.

FEC=Iron-deficiency Chlorosis=Iron Chlorosis. Plants are scored 1 to 9based on visual observations. A score of 1 indicates the plants are deador dying from iron-deficiency chlorosis, a score of 5 means plants haveintermediate health with some leaf yellowing, and a score of 9 means nostunting of the plants or yellowing of the leaves. Preliminary scoresare reported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

FEY=FROGEYE LEAF SPOT. Frogeye Leaf Spot is a fungal disease caused byCercospora sojina. Plants are evaluated using a visual fungal diseasescore from 1 to 9 comparing all genotypes in a given trial to knownresistant and susceptible checks in the trial. The score is based uponthe number and size of leaf lesions. A score of 1 indicates severe leafnecrosis lesions, whereas a score of 9 indicates no lesions. Preliminaryscores are reported as double digits, for example ‘55’ indicates apreliminary score of 5 on the scale of 1 to 9.

FLOWER COLOR. Data values include: P=purple and W=white.

GENE SILENCING. The interruption or suppression of the expression of anucleic acid sequence at the level of transcription or translation.

GENOTYPE. Refers to the genetic constitution of a cell or organism.

GPC=Grams per hundred seeds=g/100 seeds. Soybean seeds vary in seedsize. The weight in grams of 100 seeds can be used to estimate the seedrequired to plant a given area. Seed size can also impact end uses.

PLANT GROWTH HABIT. This refers to the physical appearance of a plant.It can be determinate (DET), semi-determinate (SDET), or indeterminate(INDET or IND). In soybeans, indeterminate varieties are those in whichstem growth is not limited by formation of a reproductive structure(i.e., flowers, pods and seeds) and hence growth continues throughoutflowering and during part of pod filling. The main stem will develop andset pods over a prolonged period under favorable conditions. Insoybeans, determinate varieties are those in which stem growth ceases atflowering time. Most flowers develop simultaneously, and most pods fillat approximately the same time. The terms semi-determinate andintermediate are also used to describe plant habit for plants showingstem termination intermediate between that of IND and that of DET. See,e.g., Kato, S. et al. (2015) “Seed yield and its components ofindeterminate and determinate lines in recombinant inbred lines ofsoybean.” Breed Sci 65:154-160.

HAPLOID. A cell or organism having one set of the two sets ofchromosomes in a diploid cell or organism.

HERBRES=Herbicide Resistance. This indicates that the plant is moretolerant to the herbicide or herbicide class shown as compared to thelevel of herbicide tolerance exhibited by wild type plants. Adesignation of ‘Gly’ indicates tolerance to glyphosate, a designation of‘SU’ indicates tolerance to sulfonylurea herbicides, a designation of‘ALS’ indicates tolerance to ALS-inhibiting herbicides, a designation of‘PPO’ indicates tolerance to protoporphyringogen oxidase (protox)inhibiting herbicides, a designation of ‘MET’ indicates tolerance tometribuzin, a designation of ‘AUX’ indicates tolerance to auxinherbicides, and a designation of ‘HPPD’ indicates tolerance top-hydroxyphenylpyruvate dioxygenase (HPPD) inhibiting herbicides. Adesignation of “ALS1” indicates that tolerance is conferred by thesoybean ALS1 gene, a designation of “ALS2” indicates that tolerance isconferred by the soybean ALS2 gene, and a designation of “HRA” indicatesthat tolerance is conferred by an HRA transgene.

HGT=Plant Height=Height/maturity. Plant height is taken from the top ofthe soil to the top pod of the plant and is measured in inches. Plantheight is taken at physiological maturity when 95% of pods on the mainstem have reached mature color. If the value is presented as a score ona scale of 1 to 9, 9 is tallest and 1 is shortest, with the differencefrom one score to the next being approximately 2 to 3 inches.

HIGH YIELD ENVIRONMENTS. Areas which lack normal stress, typicallyhaving sufficient rainfall, water drainage, low disease pressure, lowweed pressure, and/or uniform or low variability soil.

HILUM. This refers to the scar left on the seed which marks the placewhere the seed was attached to the pod prior to harvest. HILA COLOR datavalues include: BR=brown; TN=tan; Y=yellow; BL=black; IB=ImperfectBlack; BF=buff, G=Grey. Tan hila may also be designated as imperfectyellow (IY).

HLC=HO=High Oleic. Oil with seventy percent or more oleic acid isclassified as high oleic oil. Oleic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

HRVWT=Weight of harvested soybeans in pounds taken followingphysiological maturity when 95% of pods on the main stem have reachedmature color and adjusted to 13% moisture.

HYPLSC=Hypocotyl Length=Hypocotyl Elongation=Hypocotyl Score. This scoreindicates the ability of the seed to emerge when planted 3″ deep in sandpots and with a controlled temperature of 25° C. The number of plantsthat emerge each day are counted. Based on this data, each genotype isgiven a score from 1 to 9 based on its rate of emergence and the percentof emergence. A score of 1 indicates a very poor rate and percent ofemergence, an intermediate score of 5 indicates average ratings, and ascore of 9 indicates an excellent rate and percent of emergence.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

HYPOCOTYL. A hypocotyl is the portion of an embryo or seedling betweenthe cotyledons and the root.

HYPOCOTYL COLOR. This is the color of the hypocotyl taken approximately7 to 10 days after planting. Colors can be: G=green, GB=green withbronze, P=Purple, DP=dark purple.

LDGMID=Mid-Season Standability. The lodging resistance of plants at midseason. Lodging is rated on a scale of 1 to 9. A score of 1 indicatesplants that are lying on the ground, a score of 5 indicates plants areleaning at a 450 angle in relation to the ground, and a score of 9indicates erect plants. Preliminary scores may be reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

LDGSEV=Lodging Resistance=Harvest Standability. Lodging is rated on ascale of 1 to 9. A score of 1 indicates plants that are lying on theground, a score of 5 indicates plants are leaning at a 45 angle inrelation to the ground, and a score of 9 indicates erect plants.Preliminary scores may be reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

LEAF COLOR SCORE: This is the color of the leaves taken at the R3 to R6growth stage. Color ranges from light green, medium green and darkgreen. Number values are given on a scale of 1 to 9, with 1-3 beinglight green, 4-6 being medium green and 7-9 being dark green.

LEAFLETS. These are parts of the plant shoot involved in the manufactureof food for the plant by the process of photosynthesis.

LEAF SHAPE (LSH). This refers to the leaflet shape. Data values include:LN=linear; O=Oval; OVT=Ovate LINKAGE. Refers to a phenomenon whereinalleles on the same chromosome tend to segregate together more oftenthan expected by chance if their transmission was independent.

LINKAGE DISEQUILIBRIUM. Refers to a phenomenon wherein alleles tend toremain together in linkage groups when segregating from parents tooffspring, with a greater frequency than expected from their individualfrequencies.

LLC=Oil with three percent or less linolenic acid is classified as lowlinolenic oil. Linolenic acid is one of the five most abundant fattyacids in soybean seeds. It is measured by gas chromatography and isreported as a percent of the total oil content.

LLE=Linoleic Acid Percent. Linoleic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

LLN=Linolenic Acid Percent. Linolenic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

LOCUS. A defined segment of DNA.

LOCUS CONVERSION. Refers to seeds, plants, and/or parts thereofdeveloped by backcrossing or genetic transformation wherein essentiallyall of the desired morphological and physiological characteristics of avariety are recovered in addition to at least one locus which has beentransferred into the variety by introgression, backcrossing or genetictransformation. The locus can be a native locus, a transgenic locus, ora combination thereof.

MAT ABS=MATABS=ABSOLUTE MATURITY. This term is defined as the length oftime from planting to complete physiological development (maturity). Theperiod from planting until maturity is reached is measured in days,usually in comparison to one or more standard varieties. Plants areconsidered mature when 95% of the pods have reached their mature color.

MATURITY GROUP. This refers to an agreed-on industry division of groupsof varieties, based on the zones in which they are adapted primarilyaccording to day length or latitude. They consist of very long daylength varieties (Groups 000, 00, 0), and extend to very short daylength varieties (Groups VII, VIII, IX, X).

MST=Moisture at harvest. The actual percent of moisture in the soybeansat harvest.

NARROW ROWS. Term indicates 7″ and 15″ row spacing.

NEI DISTANCE. A quantitative measure of percent similarity between twolines. Nei's distance between lines A and B can be defined as1−((2*number alleles in common)/(number alleles in A+number alleles inB)). For example, if lines A and B are the same for 95 out of 100alleles, the Nei distance would be 0.05. If lines A and B are the samefor 98 out of 100 alleles, the Nei distance would be 0.02. Free softwarefor calculating Nei distance is available on the internet at multiplelocations. See Nei & Li (1979) Proc Natl Acad Sci USA 76:5269.

NUCLEIC ACID. An acidic, chain-like biological macromolecule consistingof multiple repeat units of phosphoric acid, sugar, and purine andpyrimidine bases.

OILPCT=% oil=OIL PERCENT=OIL (%). Soybean seeds contain a considerableamount of oil. Oil is measured by NIR spectrophotometry and is reportedas a percentage basis. The percent oil is measured at a specifiedmoisture content of the seed, and adjusted to 13% moisture (H₂O).

OIL/MEAL TYPE. Designates varieties specially developed with thefollowing oil traits: HLC=High Oleic oil (>70% oleic content); LLC=LowLinolenic (<3% linolenic content); ULC=Ultra Low Linolenic oil (<1%linolenic oil content).

OLC=OLEIC ACID PERCENT. Oleic acid is one of the five most abundantfatty acids in soybean seeds. It is measured by gas chromatography andis reported as a percent of the total oil content.

PEDIGREE DISTANCE. Relationship among generations based on theirancestral links as evidenced in pedigrees. May be measured by thedistance of the pedigree from a given starting point in the ancestry.

PERCENT IDENTITY. Percent identity as used herein refers to thecomparison of the homozygous alleles of two soybean varieties. Percentidentity is determined by comparing a statistically significant numberof the homozygous alleles of two developed varieties. For example, apercent identity of 90% between soybean variety 1 and soybean variety 2means that the two varieties have the same allele at 90% of the lociused in the comparison.

PERCENT SIMILARITY. Percent similarity as used herein refers to thecomparison of the homozygous alleles of a soybean variety such as5PYPS54 with another plant, and if the homozygous allele of 5PYPS54matches at least one of the alleles from the other plant, then they arescored as similar. Percent similarity is determined by comparing astatistically significant number of loci and recording the number ofloci with similar alleles as a percentage. A percent similarity of 90%between 5PYPS54 and another plant means that 5PYPS54 matches at leastone of the alleles of the other plant at 90% of the loci used in thecomparison.

PLANT. As used herein, the term “plant” includes reference to animmature or mature whole plant, including a plant from which seed orgrain or anthers have been removed. Any seed or embryo that will producethe plant is also considered to be the plant.

PLANT PARTS. As used herein, the term “plant part” includes a leaf,stem, root, root tip, anther, seed, grain, embryo, pollen, ovule,flower, cotyledon, hypocotyl, pod, flower, shoot, stalk, tissue, tissueculture, cell and the like. A plant part includes at least one cell,such as a somatic cell, of the plant from which the plant part wasobtained.

PLM or PALMITIC ACID PERCENT. Palmitic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

PMG infested soils. Soils containing Phytophthora sojae.

POD. This refers to the fruit of a soybean plant. It consists of thehull or shell (pericarp) and the soybean seeds. POD COLOR data valuesinclude: BR=brown; TN=tan.

POWDERY MILDEW. Powdery Mildew is caused by a fungus, Microsphaeradiffusa. Tolerance to Powdery Mildew is rated on a scale of 1 to 9, witha score of 1 being very susceptible ranging up to a score of 9 beingtolerant. Preliminary scores are reported as double digits, for example‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

PRM=PRMMAT=Predicted Relative Maturity=RM=Relative Maturity. Soybeanmaturities are divided into relative maturity groups (denoted as 000,00, 0, I, II, III, IV, V, VI, VII, VIII, IX, X, or 000, 00, 0, 1, 2, 3,4, 5, 6, 7, 8, 9, 10). Within a maturity group are sub-groups. Asub-group is a tenth of a relative maturity group (for example 1.3 wouldindicate a group 1 and subgroup 3). Within narrow comparisons, thedifference of a tenth of a relative maturity group equates very roughlyto a day difference in maturity at harvest.

PRT or PHYTOPHTHORA FIELD TOLERANCE. Tolerance to Phytophthora root rotis rated on a scale of 1 to 9, with a score of 1 indicating the plantshave no tolerance to Phytophthora, ranging to a score of 9 being thebest or highest tolerance. PRTLAB indicates the tolerance was scoredusing plants in lab assay experiments. Preliminary scores are reportedas double digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

PHYTOPHTHORA RESISTANCE GENE (Rps). Various Phytophthora resistancegenes are known and include, but are not limited to: Rps1-a=resistanceto races 1-2, 10-11, 13-18, 24; Rps1-c=resistance to races 1-3, 6-11,13, 15, 17, 21, 23, 24, 26, 28-30, 32, 34, 36; Rps1-k=resistance toraces 1-11, 13-15, 17, 18, 21-24, 26, 36, 37; Rps3-a=resistance to races1-5, 8, 9, 11, 13, 14, 16, 18, 23, 25, 28, 29, 31-35, 39-41, 43-45,47-52, 54; Rps3-c=resistance to races 1-4, 10-16, 18-36, 38-54;Rps6=resistance to races 1-4, 10, 12, 14-16, 18-21, 25, 28, 33-35; and,Rps8=resistance to races 1-5, 9, 13-15, 21, 25, 29, 32. As reported inthe tables “-” or “ ” indicates that a specific gene for resistance hasnot been identified to date.

PRO=PROTN=PROTN (%)=% Protein=PROTEIN PERCENT. Soybean seeds contain aconsiderable amount of protein. Protein is generally measured by NIRspectrophotometry, and is reported as a percent on a dry weight basis ofthe seed. The percent protein is measured at a specified moisturecontent of the seed, and adjusted to 13% moisture (H₂O).

PUBESCENCE. This refers to a covering of very fine hairs closelyarranged on the leaves, stems and pods of the soybean plant. PUBESCENCECOLOR data values include: L=Light Tawny; T=Tawny; G=Gray.

R160=Palmitic Acid percentage. Percentage of palmitic acid as determinedusing methods described in Reske et al. (1997) “TriacylglycerolComposition and Structure in Genetically Modified Sunflower and SoybeanOils” JAOCS 74:989.

R180=Stearic acid percentage. Percentage of Stearic acid as determinedusing methods described in Reske et al. (1997) JAOCS 74:989.

R181=Oleic acid percentage. Percentage of oleic acid as determined usingmethods described in Reske et al. (1997) JAOCS 74:989.

R182=Linoleic acid percentage. Percentage of linoleic acid as determinedusing methods described in Reske et al. (1997) JAOCS 74:989.

R183=Linolenic acid percentage. Percentage of linolenic acid asdetermined using methods described in Reske et al. (1997) JAOCS 74:989.

RESISTANCE. As used herein, resistance is synonymous with tolerance andis used to describe the ability of a plant to withstand exposure to aninsect, disease, herbicide, environmental stress, or other condition. Aresistant plant variety will be able to better withstand the insect,disease pathogen, herbicide, environmental stress, or other condition ascompared to a non-resistant or wild-type variety.

RKI=SOUTHERN ROOT-KNOT NEMATODE. Southern root knot nematode,Meloidogyne incognita, is a plant parasite that can cause major damageto roots, reducing yield potential. Severity is visually scored on rootsin a range from 1 to 9 comparing all genotypes in a given experiment toknown resistant and susceptible checks. The score is determined byvisually scoring the roots for presence or absence of galling in acontrolled chamber bioassay. A score of 1 indicates severe galling ofthe root system which can cause premature death from decomposition ofthe root system (susceptible). A score of 9 indicates that there islittle to no galling of the roots (resistant). Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

RKA=PEANUT ROOT-KNOT NEMATODE. Peanut root knot nematode, Meloidogynearenaria, is a plant parasite that can cause major damage to roots,reducing yield potential. Severity is visually scored on roots in arange from 1 to 9 comparing all genotypes in a given experiment to knownresistant and susceptible checks. The score is determined by visuallyscoring the roots for presence or absence of galling in a controlledchamber bioassay. A score of 1 indicates severe galling of the rootsystem which can cause pre-mature death from decomposition of the rootsystem (susceptible). A score of 9 indicates that there is little to nogalling of the roots (resistant). Preliminary scores are reported asdouble digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

RKJ=JAVANICA ROOT-KNOT NEMATODE. Javanica root knot nematode,Meloidogyne javanica, is a plant parasite that can cause major damage toroots, reducing yield potential. Severity is visually scored on roots ina range from 1 to 9 comparing all genotypes in a given experiment toknown resistant and susceptible checks. The score is determined byvisually scoring the roots for presence or absence of galling in acontrolled chamber bioassay. A score of 1 indicates severe galling ofthe root system which can cause premature death from decomposition ofthe root system (susceptible). A score of 9 indicates that there islittle to no galling of the roots (resistant). Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

SCN=SOYBEAN CYST NEMATODE RESISTANCE=Cyst Nematode Resistance=CystNematode. The score is based on resistance to a particular race ofsoybean cyst nematode (Heterodera glycines), such as race 1, 2, 3, 5 or14 to reproduce on the roots of a plant. Scores are from 1 to 9 andindicate visual observations of the number of female SCN nematodes ascompared to known susceptible genotypes in the test. A score of 1indicates the number of female SCN nematodes is greater than 71% of thenumber observed on known susceptible varieties and cause yield loss,while a score of 9 indicates the number of female SCN nematodes is lessthan 7% of the number observed on known susceptible varieties, and theline shows strong SCN resistance. Preliminary scores are reported asdouble digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

SCN Resistance Source. There are three typical sources of geneticresistance to SCN: PI88788, PI548402 (also known as Peking), andPI437654.

SCN infected soils. Soils containing soybean cyst nematode.

SD VIG or Seedling Vigor. The score is based on the speed of emergenceof the plants within a plot relative to other plots within anexperiment. A score of 1 indicates no plants have expanded first leaves,while a score of 9 indicates that 90% of plants growing have expandedfirst leaves.

SDS or SUDDEN DEATH SYNDROME. SDS is caused by the fungal pathogenformerly known as Fusarium solani f.sp. glycines, which is currentlyknown as Fusarium virguliforme (see, e.g., Aoki et al. (2003) Mycologia95:660-684). Tolerance to Sudden Death Syndrome is rated on a scale of 1to 9, with a score of 1 being very susceptible ranging up to a score of9 being tolerant. Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

SEED COAT LUSTER. Data values include D=dull; S=shiny.

SEED PROTEIN PEROXIDASE ACTIVITY. Varieties can be classified as high,low, or mixed for peroxidase activity and is scored as H=high, L=low,M=mixed. If mixed value, the percentage of high and low seeds can becalculated. For example: a variety mixed for peroxidase may have 40% ofseeds high and 60% of seeds low for peroxidase activity.

SEED SHAPE. Soybean seed shapes are measured using calipers. Shapes canbe SP=spherical, SPF=spherical flattened, E=elongate, or EF=elongateflattened.

SEED SIZE RANGE. This is the range of the average number of seeds perpound taken over different years and different locations.

SEED SIZE SCORE. This is a measure of the seed size from 1 to 9. Thehigher the score, the smaller the seed size measured. Preliminary scoresare reported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

SEPTORIA LEAF SPOT. Septoria Leaf Spot, also known as Brown Spot, iscaused by the fungus Septoria glycines. Symptoms can occur as early asV2 on lower leaves, and may move up the plant affecting leaves as wellas stems and pods in plants approaching maturity. Symptoms includeirregular dark brown spots on upper and lower leaf surfaces, or thestems or pods. Infected leaves may yellow or brown and drop early.Tolerance to Septoria Leaf Spot is rated on a scale of 1 to 9, with ascore of 1 being very susceptible ranging up to a score of 9 beingtolerant. Preliminary scores are reported as double digits, for example‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

SHATTR or Shattering. This refers to the amount of pod dehiscence priorto harvest. Pod dehiscence involves seeds falling from the pods to thesoil. This is a visual score from 1 to 9 comparing all genotypes withina given test. A score of 1 indicates 100% of the pods are opened, whilea score of 9 means pods have not opened and no seeds have fallen out.

SHOOTS. These are a portion of the body of the plant. They consist ofstems, petioles and leaves.

SOYBEAN MOSAIC VIRUS or SMV. Soybean mosaic virus (SMV) is a pathogenicplant virus which belongs to the Potyviridae family and believed to bespread by aphids. Viral infection in soybean can cause stunting ofplants as well as crinkling and mottling of leaves. Leaf blades can bepuckered along the veins and curled downward. Mottling appears as lightand dark green patches on leaves. SMV can also reduce seed size and/orpod number per plant, as well as contributing to seed discolorationassociated with the hilum. Tolerance to SMV is rated visually on a scaleof 1 to 9, with a score of 1 being very susceptible ranging up to ascore of 9 being tolerant. Preliminary scores are reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

SPLB=S/LB=Seeds per Pound. Soybean seeds vary in seed size, therefore,the number of seeds required to make up one pound also varies. Thisaffects the pounds of seed required to plant a given area, and can alsoimpact end uses.

STC or Stearic Acid Percent. Stearic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

STRESS ENVIRONMENTS. Areas which have one or more conditions that do notpermit the full expression of high yield. These conditions may be causedby biotic or abiotic stresses.

SUBLINE. Although 5PYPS54 contains substantially fixed genetics, and isphenotypically uniform and with no off-types expected, there stillremains a small proportion of segregating loci either within individualsor within the population as a whole. The segregating loci both withinany individual plant and/or the population can be used to extract uniquevarieties (sublines) with similar phenotype but improved agronomics.

TARGET SPOT. This is a fungal disease caused by Corynespora cassiicola.Symptoms usually consist of roughly circular, necrotic leaf lesionsranging in size from minute to 11 mm in diameter, though typicallyapproximately 4 to 5 mm in diameter, and with a yellow margin. Largelesions occasionally exhibit a zonate pattern associated with thisdisease. Tolerance to target spot is scored from 1 to 9 by visuallycomparing all genotypes in a given test. A score of 1 indicates completedeath of the experimental unit while a score of 9 indicates no symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

WHMD or WHITE MOLD TOLERANCE=WHITE MOLD. This is a fungal disease causedby Sclerotinia sclerotiorum that creates mycelial growth and death ofplants. Tolerance to white mold is scored from 1 to 9 by visuallycomparing all genotypes in a given test. A score of 1 indicates completedeath of the experimental unit while a score of 9 indicates no symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

VARIETY. A substantially homozygous soybean line and minor modificationsthereof that retains the overall genetics of the soybean line includingbut not limited to a subline, a locus conversion, a mutation, atransgenic, or a somaclonal variant. Variety includes seeds, plants,plant parts, and/or seed parts of the instant soybean line.

YIELD. Unless stated to the contrary, yield values are given in bushelsper acre (bu/a) at 13% moisture.

Soybean Variety 5PYPS54

Soybean variety 5PYPS54 has been self-pollinated a sufficient number ofgenerations, with careful attention to uniformity of plant type toensure a sufficient level of homozygosity and phenotypic stability. Thevariety has been increased with continued observation for uniformity. Novariant traits have been observed or are expected.

Soybean variety 5PYPS54 has shown uniformity and stability for alltraits, as described in the following variety description information. Avariety description of soybean variety 5PYPS54 is provided in Table 1.Traits reported are average values for all locations and years orsamples measured. Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

Soybean variety 5PYPS54, being substantially homozygous, can bereproduced by planting seeds of the variety, growing the resultingsoybean plants under self-pollinating or sib-pollinating conditions, andharvesting the resulting seed, using techniques familiar to theagricultural arts. Development of soybean variety 5PYPS54 is shown inthe breeding history summary in Table 3.

Genetic Marker Profile

In addition to phenotypic observations, a plant can also be identifiedby its genotype. The genotype of a plant can be characterized through agenetic marker profile which can identify plants of the same variety ora related variety, or which can be used to determine or validate apedigree. Genetic marker profiles can be obtained by techniques such asrestriction fragment length polymorphisms (RFLPs), randomly amplifiedpolymorphic DNAs (RAPDs), arbitrarily primed polymerase chain reaction(AP-PCR), DNA amplification fingerprinting (DAF), sequence characterizedamplified regions (SCARs), amplified fragment length polymorphisms(AFLPs), simple sequence repeats (SSRs) also referred to asmicrosatellites, single nucleotide polymorphisms (SNPs), or genome-wideevaluations such as genotyping-by-sequencing (GBS). For example, seeCregan et al. (1999) “An Integrated Genetic Linkage Map of the SoybeanGenome” Crop Science 39:1464, and Berry et al. (2003) “AssessingProbability of Ancestry Using Simple Sequence Repeat Profiles:Applications to Maize Inbred Lines and Soybean Varieties” Genetics165:331.

Favorable genotypes and or marker profiles, optionally associated with atrait of interest, may be identified by one or more methodologies. Insome examples one or more markers are used, including but not limited toAFLPs, RFLPs, ASH, SSRs, SNPs, indels, padlock probes, molecularinversion probes, microarrays, sequencing, and the like. In somemethods, a target nucleic acid is amplified prior to hybridization witha probe. In other cases, the target nucleic acid is not amplified priorto hybridization, such as methods using molecular inversion probes (see,for example Hardenbol et al. (2003) Nat Biotech 21:673-678). In someexamples, the genotype related to a specific trait is monitored, whilein other examples, a genome-wide evaluation including but not limited toone or more of marker panels, library screens, association studies,microarrays, gene chips, expression studies, or sequencing such aswhole-genome resequencing and genotyping-by-sequencing (GBS) may beused. In some examples, no target-specific probe is needed, for exampleby using sequencing technologies, including but not limited tonext-generation sequencing methods (see, for example, Metzker (2010) NatRev Genet 11:31-46; and, Egan et al. (2012) Am J Bot 99:175-185) such assequencing by synthesis (e.g., Roche 454 pyrosequencing, Illumina GenomeAnalyzer, and Ion Torrent PGM or Proton systems), sequencing by ligation(e.g., SOLiD from Applied Biosystems, and Polnator system from AzcoBiotech), and single molecule sequencing (SMS or third-generationsequencing) which eliminate template amplification (e.g., Helicossystem, and PacBio RS system from Pacific BioSciences). Furthertechnologies include optical sequencing systems (e.g., Starlight fromLife Technologies), and nanopore sequencing (e.g., GridION from OxfordNanopore Technologies). Each of these may be coupled with one or moreenrichment strategies for organellar or nuclear genomes in order toreduce the complexity of the genome under investigation via PCR,hybridization, restriction enzyme (see, e.g., Elshire et al. (2011) PLoSONE 6:e19379), and expression methods. In some examples, no referencegenome sequence is needed in order to complete the analysis.

Methods are provided of characterizing soybean variety 5PYPS54, or avariety comprising the phenotypic characteristics, morphologicalcharacteristics, physiological characteristics or combination thereof ofsoybean variety 5PYPS54. A method comprising isolating nucleic acids,such as DNA, from a plant, a plant part, plant cell or a seed of thesoybean variety disclosed herein is provided. The method can includemechanical, electrical and/or chemical disruption of the plant, plantpart, plant cell or seed, contacting the disrupted plant, plant part,plant cell or seed with a buffer or solvent, to produce a solution orsuspension comprising nucleic acids, optionally contacting the nucleicacids with a precipiting agent to precipitate the nucleic acids,optionally extracting the nucleic acids, and optionally separating thenucleic acids such as by centrifugation or by binding to beads or acolumn, with subsequent elution, or a combination thereof. If DNA isbeing isolated, an RNase can be included in one or more of the methodsteps. The nucleic acids isolated can comprise all or substantially allof the genomic DNA sequence, all or substantially all of the chromosomalDNA sequence or all or substantially all of the coding sequences (cDNA)of the plant, plant part, or plant cell from which they were isolated.The amount and type of nucleic acids isolated may be sufficient topermit whole genome sequencing of the plant from which they wereisolated or chromosomal marker analysis of the plant from which theywere isolated.

The methods can be used to produce nucleic acids from the plant, plantpart, seed or cell, which nucleic acids can be, for example, analyzed toproduce data. The data can be recorded. The nucleic acids from thedisrupted cell, the disrupted plant, plant part, plant cell or seed orthe nucleic acids following isolation or separation can be contactedwith primers and nucleotide bases, and/or a polymerase to facilitate PCRsequencing or marker analysis of the nucleic acids. In some examples,the nucleic acids produced can be sequenced or contacted with markers toproduce a genetic profile, a molecular profile, a marker profile, ahaplotype, or any combination thereof. In some examples, the geneticprofile or nucleotide sequence is recorded on a computer readablemedium. In other examples, the methods may further comprise using thenucleic acids produced from plants, plant parts, plant cells or seeds ina plant breeding program, for example in making soybean crossing,selection and/or advancement decisions in a breeding program. Crossingincludes any type of plant breeding crossing method, including but notlimited to outcrossing, selfing, backcrossing, locus conversion,introgression and the like.

In some examples, one or more markers are used to characterize and/orevaluate a soybean variety. Particular markers used for these purposesare not limited to any particular set of markers, but are envisioned toinclude any type of marker and marker profile which provides a means ofdistinguishing varieties. For example, one method of comparison is touse only homozygous loci for 5PYPS54.

Primers and PCR protocols for assaying these and other markers aredisclosed in Soybase (sponsored by the USDA Agricultural ResearchService and Iowa State University) which is available online. Inaddition to being used for identification of soybean variety 5PYPS54 andplant parts and plant cells of variety 5PYPS54, the genetic profile maybe used to identify a soybean plant produced through the use of 5PYPS54or to verify a pedigree for progeny plants produced through the use of5PYPS54. The genetic marker profile is also useful in breeding anddeveloping backcross conversions.

Provided is a soybean plant characterized by molecular and physiologicaldata obtained from the representative sample of said variety depositedwith the American Type Culture Collection (ATCC). Thus, plants, seeds,or parts thereof, having all or substantially all of the physiological,morphological, and/or phenotypic characteristics of soybean variety5PYPS54 are provided. Further provided is a soybean plant formed by thecombination of the disclosed soybean plant or plant cell with anothersoybean plant or cell and comprising the homozygous alleles of thevariety. A soybean plant comprising all of the physiological,morphological and/or phenotypic characteristics of soybean variety5PYPS54 can be combined with another soybean plant in a soybean breedingprogram. In some examples the other soybean plant comprises all of thephysiological, morphological and/or phenotypic characteristics ofsoybean variety 5PYPS54.

In some examples, a plant, a plant part, or a seed of soybean variety5PYPS54 is characterized by producing a molecular profile. A molecularprofile includes but is not limited to one or more genotypic and/orphenotypic profile(s). A genotypic profile includes but is not limitedto a marker profile, such as a genetic map, a linkage map, a traitmarker profile, a SNP profile, an SSR profile, a genome-wide markerprofile, a haplotype, and the like. A molecular profile may also be anucleic acid sequence profile, and/or a physical map. A phenotypicprofile includes but is not limited to one or more phenotypic traits, aprotein expression profile, a metabolic profile, an mRNA expressionprofile, and the like.

Means of performing genetic marker profiles using SSR polymorphisms arewell known in the art. A marker system based on SSRs can be highlyinformative in linkage analysis relative to other marker systems in thatmultiple alleles may be present. Another advantage of this type ofmarker is that, through use of flanking primers, detection of SSRs canbe achieved, for example, by using the polymerase chain reaction (PCR),thereby eliminating the need for labor-intensive Southern hybridization.PCR detection is done using two oligonucleotide primers flanking thepolymorphic segment of repetitive DNA to amplify the SSR region.

Following amplification, markers can be scored by electrophoresis of theamplification products. Scoring of marker genotype is based on the sizeof the amplified fragment, which correlates to the number of base pairsof the fragment. While variation in the primer used or in laboratoryprocedures can affect the reported fragment size, relative values shouldremain constant regardless of the specific primer or laboratory used.When comparing varieties it is preferable if all SSR profiles areperformed in the same lab.

Primers used are publicly available and may be found in the Soybasedatabase or Unigene database (each available online), Cregan (1999 CropScience 39:1464-1490), Choi et al. (2007 Genetics 176:685-696), andHyten et al. (2010 Crop Sci 50:960-968). See also, PCT Publication WO99/31964, U.S. Pat. Nos. 6,162,967, 7,288,386.

The SSR profile of soybean plant 5PYPS54 can be used to identify plantscomprising 5PYPS54 as a parent, since such plants will comprise the samehomozygous alleles as 5PYPS54. Because the soybean variety isessentially homozygous at all relevant loci, most loci should have onlyone type of allele present. In contrast, a genetic marker profile of anF1 progeny should be the sum of those parents, e.g., if one parent washomozygous for allele X at a particular locus, and the other parenthomozygous for allele Y at that locus, then the F1 progeny will be XY(heterozygous) at that locus. Subsequent generations of progeny producedby selection and breeding are expected to be of genotype XX(homozygous), YY (homozygous), or XY (heterozygous) for that locusposition. When the F1 plant is selfed or sibbed for successive filialgenerations, the locus should be either X or Y for that position.

In addition, plants and plant parts substantially benefiting from theuse of 5PYPS54 in their development, such as 5PYPS54 comprising abackcross conversion, transgene, or genetic sterility factor, may beidentified by having a molecular marker profile with a high percentidentity to 5PYPS54. Such a percent identity might be 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 99.9% identical to 5PYPS54.

The SSR profile of variety 5PYPS54 also can be used to identifyessentially derived varieties and other progeny varieties developed fromthe use of 5PYPS54, as well as cells and other plant parts thereof.Plants include, for example, any plant having at least 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 99.9% of the markers in theSSR profile, and that retain 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, 99%, 99.5%, or 99.9% of the physiological and morphologicalcharacteristics of variety 5PYPS54 when grown under the same conditions.Such plants may be developed, for example, using the markers identifiedin WO00/31964, U.S. Pat. Nos. 6,162,967 and 7,288,386. Progeny plantsand plant parts produced using 5PYPS54 may be identified by having amolecular marker profile of at least 25%, 30%, 35%, 40%, 45%, 50%, 55%,60%, 65%, 70%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%,86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or99.5% genetic contribution from soybean variety 5PYPS54, as measured byeither percent identity or percent similarity. Such progeny may befurther characterized as being within a pedigree distance of 5PYPS54,such as within 1, 2, 3, 4, or 5 or less cross-pollinations to a soybeanplant other than 5PYPS54, or a plant that has 5PYPS54 as a progenitor.Unique molecular profiles may be identified with other molecular toolssuch as SNPs and RFLPs.

Introduction of a New Trait or Locus into 5PYPS54

Variety 5PYPS54 represents a new genetic variety into which a locus ortrait may be introduced or introgressed. Transformation and backcrossingrepresent two methods that can be used to accomplish such anintrogression.

Provided are soybean plants further comprising a locus conversion whichplant may otherwise comprise, express or have all or essentially all ofthe morphological and physiological characteristics of the soybeanvariety 5PYPS54. In certain embodiments, the soybean plant is defined ascomprising a single locus conversion. The converted soybean plant mayotherwise comprise, express or have all or essentially all of themorphological and physiological characteristics of the soybean variety5PYPS54. By all or essentially all of the morphological andphysiological characteristics, it is meant that all of thecharacteristics of a plant are recovered that are otherwise present whencompared in the same environment, other than an occasional variant traitthat might arise during backcrossing or direct introduction of atransgene or specific genetic modification.

In certain embodiments, the single locus conversion may comprise atransgenic gene which has been introduced by genetic transformation intothe soybean variety 5PYPS54 or a progenitor thereof. In certainembodiments, the single locus conversion may comprise a dominant orrecessive allele. The locus conversion may confer potentially any traitupon the single locus converted plant, including herbicide resistance,insect resistance, resistance to bacterial, fungal, or viral disease,male fertility or sterility, and improved nutritional quality.

It is known to those of skill in the art that, by way of the techniqueof backcrossing, one or more traits may be introduced into a givenvariety while otherwise retaining essentially all of the traits of thatvariety. A backcross conversion of 5PYPS54 occurs when DNA sequences areintroduced through backcrossing with 5PYPS54 utilized as the recurrentparent. Naturally occurring, modified and transgenic DNA sequences maybe introduced through backcrossing techniques. A backcross conversionmay produce a plant with a trait or locus conversion in at least two ormore backcrosses, including at least 2 backcrosses, at least 3backcrosses, at least 4 backcrosses, at least 5 backcrosses, at least 6backcrosses or more, depending at least in part on the differencesbetween the parents of the original cross. Molecular marker assistedbreeding or selection may be utilized to reduce the number ofbackcrosses necessary to achieve the backcross conversion.

The complexity of the backcross conversion method depends on the type oftrait being transferred (a single gene or closely linked genes comparedto unlinked genes), the level of expression of the trait, the type ofinheritance (cytoplasmic or nuclear), dominant or recessive traitexpression, and the types of parents included in the cross. It isunderstood by those of ordinary skill in the art that for single genetraits that are relatively easy to classify, the backcross method iseffective and relatively easy to manage. (See Hallauer et al., in Cornand Corn Improvement, Sprague and Dudley, Third Ed. 1998). Desiredtraits that may be transferred through backcross conversion include, butare not limited to, sterility (nuclear and cytoplasmic), fertilityrestoration, nutritional enhancements, drought tolerance, nitrogenutilization, altered fatty acid profile, low phytate, industrialenhancements, disease resistance (bacterial, fungal, or viral), insectresistance, and herbicide resistance. In addition, a recombination siteitself, such as an FRT site, Lox site, or other site specificintegration site, may be inserted by backcrossing and utilized fordirect insertion of one or more genes of interest into a specific plantvariety. A single locus conversion may contain several transgenes ormodifications, such as a transgene or modification for diseaseresistance and for herbicide resistance. The gene for herbicideresistance may be used as a selectable marker and/or as a phenotypictrait. A single locus conversion of site specific integration systemallows for the integration of multiple genes at a known recombinationsite in the genome. At least one, at least two or at least three andless than ten, less than nine, less than eight, less than seven, lessthan six, less than five or less than four locus conversions may beintroduced into the plant by backcrossing, introgression ortransformation to express the desired trait, while the plant, or a plantgrown from the seed, plant part or plant cell, otherwise retains thephenotypic characteristics of the deposited seed when grown under thesame environmental conditions.

The backcross conversion may result from either the transfer of adominant allele or a recessive allele. Selection of progeny containingthe trait of interest can be accomplished by direct selection for atrait associated with a dominant allele. Transgenes transferred viabackcrossing typically function as a dominant single gene trait and arerelatively easy to classify. Selection of progeny for a trait that istransferred via a recessive allele requires growing and selfing thefirst backcross generation to determine which plants carry the recessivealleles. Recessive traits may require additional progeny testing insuccessive backcross generations to determine the presence of the locusof interest. The last backcross generation is usually selfed to givepure breeding progeny for the trait(s) being transferred, although abackcross conversion with a stably introgressed trait may also bemaintained by further backcrossing to the recurrent parent withsubsequent selection for the trait.

An example of backcrossing to introduce a trait into a starting varietyis described in U.S. Pat. No. 6,140,556. The procedure described in U.S.Pat. No. 6,140,556 can be summarized as follows: The soybean varietyknown as Williams '82 [Glycine max L. Merr.] (Reg. No. 222, PI 518671)was developed using backcrossing techniques to transfer a locuscomprising the Rps1 gene to the variety Williams (Bernard and Cremeens,1988, Crop Sci., 28:1027). Williams '82 is a composite of four resistantlines from the BC6F3 generation, which were selected from 12field-tested resistant lines from Williams x Kingwa. The varietyWilliams was used as the recurrent parent in the backcross and thevariety Kingwa was used as the source of the Rps1 locus. This gene locusconfers resistance to 19 of the 24 races of the fungal agentphytophthora root rot. The F1 or F2 seedlings from each backcross roundwere tested for resistance to the fungus by hypocotyl inoculation usingthe inoculum of race 5. The final generation was tested using inoculumof races 1 to 9. In a backcross such as this, where the desiredcharacteristic being transferred to the recurrent parent is controlledby a major gene which can be readily evaluated during the backcrossing,it is common to conduct enough backcrosses to avoid testing individualprogeny for specific traits such as yield in extensive replicated tests.In general, four or more backcrosses are used when there is noevaluation of the progeny for specific traits, such as yield. As in thisexample, lines with the phenotype of the recurrent parent may becomposited without the usual replicated tests for traits such as yield,protein or oil percentage in the individual lines. The variety Williams'82 is comparable to the recurrent parent variety Williams in its traitsexcept resistance to phytophthora rot. For example, both varieties havea relative maturity of 38, indeterminate stems, white flowers, brownpubescence, tan pods at maturity and shiny yellow seeds with black tolight black hila.

Along with selection for the trait of interest, progeny are selected forthe phenotype of the recurrent parent. The backcross is a form ofinbreeding, and the features of the recurrent parent are recovered aftersuccessive backcrosses, such as at least one, at least two, at leastthree, at least 4 or at least 5 backcrosses. The number of backcrossesnecessary can be reduced with the use of molecular markers. Otherfactors, such as a genetically similar donor parent, may also reduce thenumber of backcrosses necessary. As noted by Poehlman, backcrossing iseasiest for simply inherited, dominant, and easily recognized traits.

One process for adding or modifying a trait or locus in soybean variety5PYPS54 comprises crossing 5PYPS54 plants grown from 5PYPS54 seed withplants of another soybean variety that comprises a desired trait lackingin 5PYPS54, selecting F1 progeny plants that possess the desired traitor locus to produce selected F1 progeny plants, crossing the selectedprogeny plants back to 5PYPS54 plants to produce backcross1 (BC1)progeny plants. The BC1 F1 progeny plants that have the desired traitand the morphological characteristics of soybean variety 5PYPS54 areselected and backcrossed to 5PYPS54 to generate BC2F1 progeny plants.Additional backcrossing and selection of progeny plants with the desiredtrait will produce BC3F1, BC4F1, BC5F1, . . . BCxF1 generations ofplants. The backcross populations of 5PYPS54 may be furthercharacterized as having the phenotypic, physiological and/ormorphological characteristics of soybean variety 5PYPS54, such as listedin Table 1, as determined at the 5% significance level when grown in thesame environmental conditions and/or may be characterized by percentsimilarity or identity to 5PYPS54 as determined by SSR or othermolecular markers. The above method may be utilized with fewerbackcrosses in appropriate situations, such as when the donor parent ishighly related or molecular markers are used in one or more selectionsteps. Desired traits that may be used include those nucleic acids knownin the art, some of which are listed herein, that will affect traitsthrough nucleic acid expression or inhibition. Desired loci also includethe introgression of FRT, Lox, and/or other recombination sites for sitespecific integration. Desired loci further include QTLs, which may alsoaffect a desired trait.

In addition, the above process and other similar processes describedherein may be used to produce first generation progeny soybean seed byadding a step at the end of the process that comprises crossing 5PYPS54with the introgressed trait or locus with a different soybean plant andharvesting the resultant first generation progeny soybean seed.

Transgenes and transformation methods provide means to engineer thegenome of plants to contain and express heterologous genetic elements,including but not limited to foreign genetic elements, additional copiesof endogenous elements, and/or modified versions of native or endogenousgenetic elements, in order to alter at least one trait of a plant in aspecific manner. Any heterologous DNA sequence(s), whether from adifferent species or from the same species, which are inserted into thegenome using transformation, backcrossing, or other methods known to oneof skill in the art are referred to herein collectively as transgenes.The sequences are heterologous based on sequence source, location ofintegration, operably linked elements, or any combination thereof. Oneor more transgenes of interest can be introduced into soybean variety5PYPS54. Transgenic variants of soybean variety 5PYPS54 plants, seeds,cells, and parts thereof or derived therefrom are provided. Transgenicvariants of 5PYPS54 comprise the physiological and morphologicalcharacteristics of soybean variety 5PYPS54, such as listed in Table 1 asdetermined at the 5% significance level when grown in the sameenvironmental conditions, and/or may be characterized or identified bypercent similarity or identity to 5PYPS54 as determined by SSR or othermolecular markers. In some examples, transgenic variants of soybeanvariety 5PYPS54 are produced by introducing at least one transgene ofinterest into soybean variety 5PYPS54 by transforming 5PYPS54 with apolynucleotide comprising the transgene of interest. In other examples,transgenic variants of soybean variety 5PYPS54 are produced byintroducing at least one transgene by introgressing the transgene intosoybean variety 5PYPS54 by crossing.

In one example, a process for modifying soybean variety 5PYPS54 with theaddition of a desired trait, said process comprising transforming asoybean plant of variety 5PYPS54 with a transgene that confers a desiredtrait is provided. Therefore, transgenic 5PYPS54 soybean cells, plants,plant parts, and seeds produced from this process are provided. In someexamples one more desired traits may include traits such as herbicideresistance, insect resistance, disease resistance, decreased phytate,modified fatty acid profile, modified fatty acid content, carbohydratemetabolism, protein content, or oil content. The specific gene may beany known in the art or listed herein, including but not limited to apolynucleotide conferring resistance to an ALS-inhibitor herbicide,imidazolinone, sulfonylurea, protoporphyrinogen oxidase (PPO)inhibitors, hydroxyphenyl pyruvate dioxygenase (HPPD) inhibitors,glyphosate, glufosinate, triazine, 2,4-dichlorophenoxyacetic acid(2,4-D), dicamba, broxynil, metribuzin, or benzonitrile herbicides; apolynucleotide encoding a Bacillus thuringiensis polypeptide, apolynucleotide encoding a phytase, a fatty acid desaturase (e.g., FAD-2,FAD-3), galactinol synthase, a raffinose synthetic enzyme; or apolynucleotide conferring resistance to soybean cyst nematode, brownstem rot, Phytophthora root rot, soybean mosaic virus, sudden deathsyndrome, or other plant pathogen.

Numerous methods for plant transformation have been developed, includingbiological and physical plant transformation protocols. See, forexample, Miki et al., “Procedures for Introducing Foreign DNA intoPlants” in Methods in Plant Molecular Biology and Biotechnology, Glick,B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages67-88; and Armstrong (1999) “The First Decade of Maize Transformation: AReview and Future Perspective” Maydica 44:101-109. In addition,expression vectors and in vitro culture methods for plant cell or tissuetransformation and regeneration of plants are available. See, forexample, Gruber et al., “Vectors for Plant Transformation” in Methods inPlant Molecular Biology and Biotechnology, Glick, B. R. and Thompson, J.E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages 89-119.

In general, methods to transform, modify, edit or alter plant endogenousgenomic DNA include altering the plant native DNA sequence or apre-existing transgenic sequence including regulatory elements, codingand non-coding sequences. These methods can be used, for example, totarget nucleic acids to pre-engineered target recognition sequences inthe genome. Such pre-engineered target sequences may be introduced bygenome editing or modification. As an example, a genetically modifiedplant variety is generated using “custom” or engineered endonucleasessuch as meganucleases produced to modify plant genomes (see e.g., WO2009/114321; Gao et al. (2010) Plant Journal 1:176-187). Anothersite-directed engineering method is through the use of zinc fingerdomain recognition coupled with the restriction properties ofrestriction enzyme. See e.g., Urnov, et al., (2010) Nat Rev Genet. 11(9):636-46; Shukla, et al., (2009) Nature 459 (7245):437-41. Atranscription activator-like (TAL) effector-DNA modifying enzyme (TALEor TALEN) is also used to engineer changes in plant genome. See e.g.,US20110145940, Cermak et al., (2011) Nucleic Acids Res. 39(12) and Bochet al., (2009), Science 326(5959): 1509-12. Site-specific modificationof plant genomes can also be performed using the bacterial type IICRISPR (clustered regularly interspaced short palindromic repeats)/Cas(CRISPR-associated) system. See e.g., Belhaj et al., (2013), PlantMethods 9: 39; The Cas9/guide RNA-based system allows targeted cleavageof genomic DNA guided by a customizable small noncoding RNA in plants(see e.g., WO 2015026883A1).

The modified variety 5PYPS54 or a plant otherwise derived from variety5PYPS54 may be further characterized as having all or essentially all ofthe phenotypic characteristics, or all or essentially all of themorphological and physiological characteristics of variety 5PYPS54,and/or may be characterized by percent identity to 5PYPS54 as determinedby molecular markers, such as SSR markers or SNP markers. By essentiallyall of the phenotypic characteristics or morphological and physiologicalcharacteristics, it is meant that all of the characteristics of a plantare recovered that are otherwise present when compared in the sameenvironment, other than an occasional variant trait that might ariseduring backcrossing or direct introduction of a transgene or specificgenetic modification.

Plant transformation methods may involve the construction of anexpression vector. Such a vector or recombinant construct comprises aDNA sequence that contains a coding sequence, such as a protein and/orRNA coding sequence under the control of or operatively linked to aregulatory element, for example a promoter. The vector or construct maycontain one or more coding sequences and one or more regulatoryelements.

A genetic trait which has been engineered into the genome of aparticular soybean plant may then be moved into the genome of anothervariety using traditional breeding techniques that are well known in theplant breeding arts. For example, a backcrossing approach is commonlyused to move a transgene from a transformed soybean variety into anelite soybean variety, and the resulting backcross conversion plantwould then contain the transgene(s).

Various genetic elements can be introduced into the plant genome usingtransformation. These elements include, but are not limited to genes;coding sequences; inducible, constitutive, and tissue specificpromoters; enhancing sequences; and signal and targeting sequences.

A genetic map can be generated that identifies the approximatechromosomal location of the integrated DNA molecule, for example viaconventional restriction fragment length polymorphisms (RFLP),polymerase chain reaction (PCR) analysis, simple sequence repeats (SSR),and single nucleotide polymorphisms (SNP). For exemplary methodologiesin this regard, see Glick and Thompson, Methods in Plant MolecularBiology and Biotechnology, pp. 269-284 (CRC Press, Boca Raton, 1993).

Wang et al. discuss “Large Scale Identification, Mapping and Genotypingof Single-Nucleotide Polymorphisms in the Human Genome”, Science (1998)280:1077-1082, and similar capabilities are increasingly available forthe soybean genome. Map information concerning chromosomal location isuseful for proprietary protection of a subject transgenic plant. Ifunauthorized propagation is undertaken and crosses made with othergermplasm, the map of the integration region can be compared to similarmaps for suspect plants to determine if the latter have a commonparentage with the subject plant. Map comparisons could involvehybridizations, RFLP, PCR, SSR, sequencing or combinations thereof, allof which are conventional techniques. SNPs may also be used alone or incombination with other techniques.

Likewise, plants can be genetically engineered to express variousphenotypes of agronomic interest. Through the transformation of soybeanthe expression of genes can be altered to enhance disease resistance,insect resistance, herbicide resistance, agronomic, grain quality, andother traits. Transformation can also be used to insert DNA sequenceswhich control or help control male-sterility. DNA sequences native tosoybean as well as non-native DNA sequences can be transformed intosoybean and used to alter levels of native or non-native proteins.Various promoters, targeting sequences, enhancing sequences, and otherDNA sequences can be inserted into the genome for the purpose ofaltering the expression of proteins. Reduction of the activity ofspecific genes (also known as gene silencing or gene suppression) isdesirable for several aspects of genetic engineering in plants.

Many techniques for gene silencing are well known to one of skill in theart, including but not limited to, knock-outs (such as by insertion of atransposable element such as mu (Vicki Chandler, The Maize Handbook Ch.118 (Springer-Verlag 1994)); antisense technology (see, e.g., U.S. Pat.Nos. 5,107,065; 5,453,566; and 5,759,829); co-suppression (e.g., Taylor(1997) Plant Cell 9:1245; Jorgensen (1990) Trends Biotech 8:340-344;Flavell (1994) PNAS USA 91:3490-3496; Finnegan et al. (1994)Bio/Technology 12:883-888; and Neuhuber et al. (1994) Mol Gen Genet244:230-241); RNA interference (Napoli et al. (1990) Plant Cell2:279-289; U.S. Pat. No. 5,034,323; Sharp (1999) Genes Dev 13:139-141;Zamore et al. (2000) Cell 101:25-33; and Montgomery et al. (1998) PNASUSA 95:15502-15507); virus-induced gene silencing (Burton et al. (2000)Plant Cell 12:691-705; Baulcombe (1999) Curr Op Plant Biol 2:109-113);target-RNA-specific ribozymes (Haseloff et al. (1988) Nature 334:585-591); hairpin structures (Smith et al. (2000) Nature 407:319-320;WO99/53050; WO98/53083); microRNA (Aukerman & Sakai (2003) Plant Cell15:2730-2741); ribozymes (Steinecke et al. (1992) EMBO J 11:1525;Perriman et al. (1993) Antisense Res Dev 3:253); oligonucleotidemediated targeted modification (e.g., WO03/076574 and WO99/25853);Zn-finger targeted molecules (e.g., WO01/52620; WO03/048345; andWO00/42219); use of exogenously applied RNA (e.g., US20110296556); andother methods or combinations of the above methods known to those ofskill in the art.

Exemplary nucleotide sequences and/or native loci that confer at leastone trait of interest, which optionally may be conferred or altered bygenetic engineering, transformation or introgression of a transformedevent include, but are not limited to, those categorized below.

1. Genes that Confer Resistance to Insects or Disease and that Encode:

(A) Plant disease resistance genes. Plant defenses are often activatedby specific interaction between the product of a disease resistance gene(R) in the plant and the product of a corresponding avirulence (Avr)gene in the pathogen. A plant variety can be transformed with clonedresistance gene to engineer plants that are resistant to specificpathogen strains. A plant resistant to a disease is one that is moreresistant to a pathogen as compared to the wild type plant. See, forexample U.S. Pat. No. 9,169,489, disclosing soybean plants expressing asoybean homolog of glycine-rich protein 7 (GRP7) and providing increasedinnate immunity.

Examples of fungal diseases on leaves, stems, pods and seeds include,for example, Alternaria leaf spot (Alternaria spec. atrans tenuissima),Anthracnose (Colletotrichum gloeosporoides dematium var. truncatum),brown spot (Septoria glycines), cercospora leaf spot and blight(Cercospora kikuchii), Choanephora leaf blight (Choanephorainfiindibulifera trispora (Syn.)), Dactuliophora leaf spot(Dactuliophora glycines), downy mildew (Peronospora manshurica),Drechslera blight (Drechslera glycini), frogeye leaf spot (Cercosporasojina), Leptosphaerulina leaf spot (Leptosphaerulina trifolii),Phyllostica leaf spot (Phyllosticta sojaecola), pod and stem blight(Phomopsis sojae), powdery mildew (Microsphaera diffusa), Pyrenochaetaleaf spot (Pyrenochaeta glycines), Rhizoctonia aerial, foliage, and webblight (Rhizoctonia solani), rust (Phakopsora pachyrhizi, Phakopsorameibomiae), scab (Sphaceloma glycines), Stemphylium leaf blight(Stemphylium botryosum), target spot (Corynespora cassiicola).

Examples of fungal diseases on roots and the stem base include, forexample, black root rot (Calonectria crotalariae), charcoal rot(Macrophomina phaseolina), Fusarium blight or wilt, root rot, and podand collar rot (Fusarium oxysporum, Fusarium orthoceras, Fusariumsemitectum, Fusarium equiseti), Mycoleptodiscus root rot(Mycoleptodiscus terrestris), Neocosmospora (Neocosmospora vasinfecta),pod and stem blight (Diaporthe phaseolorum), stem canker (Diaporthephaseolorum var. caulivora), Phytophthora rot (Phytophthora megasperma),brown stem rot (Phialophora gregata), Pythium rot (Pythiumaphanidermatum, Pythium irregulare, Pythium debaryanum, Pythiummyriotylum, Pythium ultimum), Rhizoctonia root rot, stem decay, anddamping-off (Rhizoctonia solani), Sclerotinia stem decay (Sclerotiniasclerotiorum), Sclerotinia southern blight (Sclerotinia rolfsii),Thielaviopsis root rot (Thielaviopsis basicola).

(B) A Bacillus thuringiensis (Bt) protein, a derivative thereof or asynthetic polypeptide modeled thereon. Non-limiting examples of Bttransgenes being genetically engineered are given in the followingpatents and patent applications: U.S. Pat. Nos. 5,188,960; 5,689,052;5,880,275; 5,986,177; 7,105,332; 7,208,474; WO91/14778; WO99/31248;WO01/12731; WO99/24581; WO97/40162; US2002/0151709; US2003/0177528;US2005/0138685; US/20070245427; US2007/0245428; US2006/0241042;US2008/0020966; US2008/0020968; US2008/0020967; US2008/0172762;US2008/0172762; and US2009/0005306.

(C) An insect-specific hormone or pheromone such as an ecdysteroid orjuvenile hormone, a variant thereof, a mimetic based thereon, or anantagonist or agonist thereof. (D) An insect-specific peptide which,upon expression, disrupts the physiology of the affected pest.

(E) An enzyme responsible for a hyperaccumulation of a monoterpene, asesquiterpene, a steroid, hydroxamic acid, a phenylpropanoid derivative,or another non-protein molecule with insecticidal activity.

(F) An enzyme involved in the modification, including thepost-translational modification, of a biologically active molecule; forexample, a glycolytic enzyme, a proteolytic enzyme, a lipolytic enzyme,a nuclease, a cyclase, a transaminase, an esterase, a hydrolase, aphosphatase, a kinase, a phosphorylase, a polymerase, an elastase, achitinase and a glucanase, whether natural or synthetic. See, forexample, International Publication WO93/02197, U.S. Pat. Nos. 6,563,020;7,145,060; and 7,087,810.

(G) A molecule that stimulates signal transduction, such as calmodulin.

(H) A hydrophobic moment peptide, such as peptides based on cecropins(cecropin A or B), magainins, melittin, tachyplesin (see InternationalPublication WO95/16776 and U.S. Pat. No. 5,580,852 disclosing peptidederivatives of tachyplesin which inhibit fungal plant pathogens), andsynthetic antimicrobial peptides that confer disease resistance (see,e.g. International Publication WO95/18855 and U.S. Pat. No. 5,607,914).

(I) A membrane permease, a channel former, or a channel blocker.

(J) A viral-invasive protein or a complex toxin derived therefrom. Forexample, the accumulation of viral coat proteins in transformed plantcells imparts resistance to viral infection and/or disease developmenteffected by the virus from which the coat protein gene is derived, aswell as by related viruses.

(K) An insect-specific antibody or an immunotoxin derived therefrom.Thus, an antibody targeted to a critical metabolic function in theinsect gut would inactivate an affected enzyme, killing the insect.

(L) A virus-specific or pathogen protein specific antibody. See, forexample, Safarnejad, et al. (2011) Biotechnology Advances 29(6):961-971, reviewing antibody-mediated resistance against plant pathogens.

(M) A developmental-arrestive protein produced in nature by a pathogenor a parasite. For example, fungal endo alpha-1,4-D-polygalacturonasesfacilitate fungal colonization and plant nutrient release bysolubilizing plant cell wall homo-alpha-1,4-D-galacturonase. See Lamb etal. (1992) Bio/Technology 10:1436. The cloning and characterization of agene which encodes a bean endopolygalacturonase-inhibiting protein isdescribed by Toubart et al. (1992) Plant J 2:367.

(N) A developmental-arrestive protein produced in nature by a plant. Forexample, Li et al., (2004) Biologica Plantarum 48(3): 367-374 describethe production of transgenic soybean plants expressing both thechitinase (chi) and the barley ribosome-inactivating gene (rip).

(O) Genes involved in the systemic acquired resistance (SAR) responseand/or the pathogenesis related genes. See Fu et al. (2013) Annu RevPlant Biol. 64:839-863, Luna et al. (2012) Plant Physiol. 158:844-853,Pieterse & Van Loon (2004) Curr Opin Plant Bio 7:456-64; and Somssich(2003) Cell 113:815-816.

(P) Antifungal genes (Ceasar et al. (2012) Biotechnol Lett 34:995-1002;Bushnell et al. (1998) Can J Plant Path 20:137-149. Also, see US PatentApplication Publications US2002/0166141; US2007/0274972; US2007/0192899;US2008/0022426; and U.S. Pat. Nos. 6,891,085; 7,306,946; and 7,598,346.

(Q) Detoxification genes, such as for fumonisin, beauvericin,moniliformin, zearalenone, and their structurally related derivatives.For example, see Schweiger et al. (2013) Mol Plant Microbe Interact.26:781-792 and U.S. Pat. Nos. 5,716,820; 5,792,931; 5,798,255;5,846,812; 6,083,736; 6,538,177; 6,388,171; and 6,812,380.

(R) Cystatin and cysteine proteinase inhibitors. See, for example,Popovic et al. (2013) Phytochemistry 94:53-59. van der Linde et al.(2012) Plant Cell 24:1285-1300 and U.S. Pat. No. 7,205,453.

(S) Defensin genes. See, for example, De Coninck et al. (2013) FungalBiology Reviews 26: 109-120, International Patent PublicationWO03/000863 and U.S. Pat. Nos. 6,911,577; 6,855,865; 6,777,592; and7,238,781.

(T) Genes conferring resistance to nematodes. See, e.g., Davies et al.(2015) Nematology 17: 249-263, Cook et al. (2012) Science 338.6111:1206-1209, Liu et al. (2012): Nature 492.7428:256-260 and InternationalPatent Publications WO96/30517; WO93/19181; WO03/033651; and Urwin etal. (1998) Planta 204:472-479; Williamson (1999) Curr Opin Plant Bio2:327-331; and U.S. Pat. Nos. 6,284,948 and 7,301,069; 8,198,509;8,304,609; and publications US2009/0064354 and US2013/0047301.

(U) Genes that confer resistance to Phytophthora Root Rot, such as Rps1,Rps1-a, Rps1-b, Rps1-c, Rps1-d, Rps1-e, Rps1-k, Rps2, Rps3-a, Rps3-b,Rps3-c, Rps4, Rps5, Rps6, Rps7, Rps8, and other Rps genes. See, forexample, Zhang et al. (2014) Crop Science 54.2: 492-499, Lin et al.(2013), Theoretical and applied genetics 126.8: 2177-2185.

(V) Genes that confer resistance to Brown Stem Rot, such as described inU.S. Pat. Nos. 9,095,103, 5,689,035 and 5,948,953.

2. Genes that Confer Resistance to a Herbicide, for Example:

(A) A herbicide that inhibits the growing point or meristem, such as animidazolinone, or a sulfonylurea. Exemplary genes include mutant ALS andAHAS enzymes. See, e.g., U.S. Pat. Nos. 5,084,082; 5,605,011; 5,013,659;5,141,870; 5,767,361; 5,731,180; 5,304,732; 4,761,373; 5,331,107;5,928,937; and 5,378,824; US Patent Publication Nos. 2007/0214515 andUS2013/0254944; and PCT Publication No. WO96/33270.

(B) Glyphosate (resistance imparted by mutant5-enolpyruvl-3-phosphikimate synthase (EPSP) and aroA genes,respectively) and other phosphono compounds such as glufosinate(phosphinothricin acetyl transferase (PAT) and Streptomyceshygroscopicus phosphinothricin acetyl transferase (bar) genes), andpyridinoxy or phenoxy proprionic acids and cyclohexones (ACCaseinhibitor-encoding genes). See, for example, U.S. Pat. No. 4,940,835,which discloses the nucleotide sequence of a form of EPSPS which canconfer glyphosate resistance. U.S. Pat. No. 5,627,061 also describesgenes encoding EPSPS enzymes. For other polynucleotides and/or methodsor uses see also U.S. Pat. Nos. 6,566,587; 6,338,961; 6,248,876;6,040,497; 5,804,425; 5,633,435; 5,145,783; 4,971,908; 5,312,910;5,188,642; 4,940,835; 5,866,775; 6,225,114; 6,130,366; 5,310,667;4,535,060; 4,769,061; 5,633,448; 5,510,471; RE 36,449; RE 37,287;7,608,761; 7,632,985; 8,053,184; 6,376,754; 7,407,913; and 5,491,288;EP1173580; WO01/66704; EP1173581; US2012/0070839; US2005/0223425;US2007/0197947; US2010/0100980; US2011/0067134; and EP1173582.Glyphosate resistance is also imparted to plants that express a genethat encodes a glyphosate oxido-reductase enzyme as described more fullyin U.S. Pat. Nos. 5,776,760 and 5,463,175. In addition, glyphosateresistance can be imparted to plants by the overexpression of genesencoding glyphosate N-acetyltransferase. See, for example,US2004/0082770; US2005/0246798; and US2008/0234130. A DNA moleculeencoding a mutant aroA gene can be obtained under ATCC accession No.39256, and the sequence of the mutant gene is disclosed in U.S. Pat. No.4,769,061. European Patent Application No. 0 333 033 and U.S. Pat. No.4,975,374 disclose nucleotide sequences of glutamine synthetase geneswhich confer resistance to herbicides such as L-phosphinothricin. Thenucleotide sequence of a phosphinothricin-acetyltransferase gene isprovided in European Patents 0 242 246 and 0 242 236. See also, U.S.Pat. Nos. 5,969,213; 5,489,520; 5,550,318; 5,874,265; 5,919,675;5,561,236; 5,648,477; 5,646,024; 6,177,616; and 5,879,903. Exemplarygenes conferring resistance to phenoxy proprionic acids andcyclohexones, such as sethoxydim and haloxyfop, are the Acc1-S1,Acc1-S2, and Acc1-S3 genes described by Marshall et al. (1992) TheorAppl Genet 83:435.

(C) A herbicide that inhibits photosynthesis, such as a triazine (psbAand gs+ genes) and a benzonitrile (nitrilase gene). Przibilla et al.(1991) Plant Cell 3:169, describe the transformation of Chlamydomonaswith plasmids encoding mutant psbA genes. Nucleotide sequences fornitrilase genes are disclosed in U.S. Pat. No. 4,810,648, and DNAmolecules containing these genes are available under ATCC Accession Nos.53435, 67441, and 67442. Cloning and expression of DNA coding for aglutathione S-transferase is described by Hayes et al. (1992) Biochem J285:173.

(D) A gene encoding a chimeric protein of rat cytochrome P4507A1 andyeast NADPH-cytochrome P450 oxidoreductase (Shiota et al. (1994) PlantPhysiol 106:17), genes for glutathione reductase and superoxidedismutase (Aono et al. (1995) Plant Cell Physiol 36:1687), and genes forvarious phosphotransferases (Datta et al. (1992) Plant Mol Biol 20:619).

(E) Protoporphyrinogen oxidase (protox or PPO) targeting herbicides. PPOis necessary for the production of chlorophyll and serves as the targetfor a variety of herbicidal compounds. PPO-inhibitor herbicides caninhibit growth of all the different species of plants present, causingtheir total destruction. The development of plants containing alteredprotox activity which are resistant to these herbicides are described,for example, in U.S. Pat. Nos. 6,288,306; 6,282,837; and 5,767,373; andWO01/12825.

(F) Genes that confer resistance to auxin or synthetic auxin herbicides.For example, an aryloxyalkanoate dioxygenase (AAD) gene may conferresistance to arlyoxyalkanoate herbicides, such as 2,4-D, as well aspyridyloxyacetate herbicides, such as described in U.S. Pat. No.8,283,522, and US2013/0035233. In other examples, a dicambamonooxygenase (DMO) is used to confer resistance to dicamba. Otherpolynucleotides of interest related to auxin herbicides and/or usesthereof include, for example, the descriptions found in U.S. Pat. Nos.8,119,380; 7,812,224; 7,884,262; 7,855,326; 7,939,721; 7,105,724;7,022,896; 8,207,092; US2011/067134; and US2010/0279866.

(G) Genes that confer resistance to glufosinate containing herbicides.Examples include genes that confer resistance to LIBERTY®, BASTA™,RELY™, FINALE™, IGNITE™, and CHALLENGE™ herbicides. Gene examplesinclude the pat gene, for example as disclosed in U.S. Pat. No.8,017,756 which describes event A5547-127. In other examples, methodsinclude the use of one or more chemicals to control weeds, see, e.g.,U.S. Pat. No. 7,407,913.

(H) Genes that confer resistance to dicamba(3,6-dichloro-2-methoxybenzoic acid), which is an organochloridederivative of benzoic acid and functions by increasing plant growth ratesuch that the plant dies.

3. Genes that Confer or Contribute to a Grain and/or SeedCharacteristic, Such as:

(A) Fatty acid profile(s), for example, by

-   -   (1) Down-regulation of stearoyl-ACP desaturase to increase        stearic acid content of the plant. See Knultzon et al. (1992)        PNAS USA 89:2624; and WO99/64579 (Genes for Desaturases to Alter        Lipid Profiles in Corn).    -   (2) Elevating oleic acid via FAD-2 gene modification and/or        decreasing linolenic acid via FAD-3 gene modification (see U.S.        Pat. Nos. 6,063,947; 6,323,392; 6,372,965; and International        Publication WO93/11245).    -   (3) Altering conjugated linolenic or linoleic acid content, such        as in WO01/12800.    -   (4) Altering LEC1, AGP, mi1ps, and various Ipa genes such as        Ipa1, Ipa3, hpt or hggt. For example, see WO02/42424;        WO98/22604; WO03/011015; U.S. Pat. Nos. 6,423,886; 6,197,561;        and, 6,825,397; US2003/0079247; US2003/0204870; WO02/057439;        WO03/011015; and Rivera-Madrid et al. (1995) PNAS USA        92:5620-5624.

B) Altered phosphate content, for example, by:

-   -   (1) Introduction of a phytase-encoding gene would enhance        breakdown of phytate, adding more free phosphate to the        transformed plant. For example, see Van Hartingsveldt et        al. (1993) Gene 127:87, for a disclosure of the nucleotide        sequence of an Aspergillus niger phytase gene.    -   (2) Modulating a gene that reduces phytate content. For example        in maize this could be accomplished by cloning and then        re-introducing DNA associated with one or more of the alleles,        such as the LPA alleles, identified in maize mutants        characterized by low levels of phytic acid, such as in        WO05/113778; and/or by altering inositol kinase activity as in        WO02/059324; U.S. Pat. No. 7,067,720; WO03/027243;        US2003/0079247; WO99/05298; U.S. Pat. Nos. 6,197,561; 6,291,224;        and 6,391,348; WO98/45448; WO99/55882; and WO01/04147.

(C) Altered carbohydrates, for example, in U.S. Pat. No. 6,232,529(method of producing high oil seed by modification of starch levels(AGP). In other examples the genes relate to altered stachyose orraffinose levels in soybean, including, for example, those described inU.S. Pat. No. 8,471,107; WO93/007742; and WO98/045448. The fatty acidmodification genes mentioned herein may also be used to affect starchcontent and/or composition through the interrelationship of the starchand oil pathways.

(D) Altered antioxidant content or composition, such as alteration oftocopherol or tocotrienols. For example, see U.S. Pat. Nos. 6,787,683;7,154,029; and WO00/68393 involving the manipulation of antioxidantlevels, and WO03/082899 through alteration of a homogentisate geranylgeranyl transferase (hggt).

(E) Altered essential seed amino acids. For example, see U.S. Pat. No.6,127,600 (method of increasing accumulation of essential amino acids inseeds); U.S. Pat. No. 6,080,913 (binary methods of increasingaccumulation of essential amino acids in seeds); U.S. Pat. No. 5,990,389(high lysine); WO99/40209 (alteration of amino acid compositions inseeds); WO99/29882 (methods for altering amino acid content ofproteins); U.S. Pat. No. 5,850,016 (alteration of amino acidcompositions in seeds); WO98/20133 (proteins with enhanced levels ofessential amino acids); U.S. Pat. No. 5,885,802 (high methionine); U.S.Pat. No. 5,885,801 (high threonine); U.S. Pat. No. 6,664,445 (plantamino acid biosynthetic enzymes); U.S. Pat. No. 6,459,019 (increasedlysine and threonine); U.S. Pat. No. 6,441,274 (plant tryptophansynthase beta subunit); U.S. Pat. No. 6,346,403 (methionine metabolicenzymes); U.S. Pat. No. 5,939,599 (high sulfur); U.S. Pat. No. 5,912,414(increased methionine); WO98/56935 (plant amino acid biosyntheticenzymes); WO98/45458 (engineered seed protein having higher percentageof essential amino acids); WO98/42831 (increased lysine); U.S. Pat. No.5,633,436 (increasing sulfur amino acid content); U.S. Pat. No.5,559,223 (synthetic storage proteins with defined structure containingprogrammable levels of essential amino acids); WO96/01905 (increasedthreonine); WO95/15392 (increased lysine); U.S. Pat. Nos. 6,930,225;7,179,955; 6,803,498; US2004/0068767; and WO01/79516.

(F) Altered amounts of protein and fatty acid in the seed.

DGAT, SUT 4, ODP1, LEC1, PGM,

4. Genes that Control Male-Sterility

There are several methods of conferring genetic male sterilityavailable, such as multiple mutant genes at separate locations withinthe genome that confer male sterility, as disclosed in U.S. Pat. Nos.4,654,465 and 4,727,219 to Brar et al., and chromosomal translocationsas described by Patterson in U.S. Pat. Nos. 3,861,709 and 3,710,511. Inaddition to these methods, Albertsen et al. U.S. Pat. No. 5,432,068,describe a system of nuclear male sterility which includes: identifyinga gene which is critical to male fertility; silencing this native genewhich is critical to male fertility; removing the native promoter fromthe essential male fertility gene and replacing it with an induciblepromoter; inserting this genetically engineered gene back into theplant; and thus creating a plant that is male sterile because theinducible promoter is not “on” resulting in the male fertility gene notbeing transcribed. Fertility is restored by inducing, or turning “on”,the promoter, which in turn allows the gene conferring male fertility tobe transcribed. Male sterile soybean lines and characterization arediscussed in Palmer (2000) Crop Sci 40:78-83, and Jin et al. (1997) SexPlant Reprod 10:13-21.

(A) Introduction of a deacetylase gene under the control of atapetum-specific promoter and with the application of the chemicalN-Ac-PPT (WO01/29237).

(B) Introduction of various stamen-specific promoters (WO92/13956 andWO92/13957).

(C) Introduction of the barnase and the barstar gene (Paul et al. (1992)Plant Mol Biol 19:611-622).

For additional examples of nuclear male and female sterility systems andgenes, see also, U.S. Pat. Nos. 5,859,341; 6,297,426; 5,478,369;5,824,524; 5,850,014; and 6,265,640.

5. Polynucleotides comprising a sequence for site specific DNArecombination. This includes the introduction of at least one FRT sitethat may be used in the FLP/FRT system and/or a Lox site that may beused in the Cre/Lox system. For example, see Lyznik et al. (2003) PlantCell Rep 21:925-932; and WO99/25821. Other systems that may be usedinclude the Gin recombinase of phage Mu (Maeser et al. (1991) Mol GenGenet 230:170-176); the Pin recombinase of E. coli (Enomoto et al.(1983) J Bacteriol 156:663-668); and the R/RS system of the pSR1 plasmid(Araki et al. (1992) J Mol Biol 182:191-203).6. Genes that affect abiotic stress resistance (including but notlimited to flowering, flower development, pod, and seed development,enhancement of nitrogen utilization efficiency, altered nitrogenresponsiveness, drought resistance or tolerance, cold resistance ortolerance, and salt resistance or tolerance) and increased yield understress. For example, see WO00/73475 where water use efficiency isaltered through alteration of malate; U.S. Pat. Nos. 5,892,009;5,965,705; 5,929,305; 5,891,859; 6,417,428; 6,664,446; 6,706,866;6,717,034; and 6,801,104; WO00/060089; WO01/026459; WO00/1035725;WO01/034726; WO01/035727; WO00/1036444; WO01/036597; WO01/036598;WO00/2015675; WO02/017430; WO02/077185; WO02/079403; WO03/013227;WO03/013228; WO03/014327; WO04/031349; WO04/076638; WO98/09521; andWO99/38977 describing genes, including CBF genes (C-repeat/DRE-BindingFactor, see, e.g., Stockinger et al. 1997 PNAS 94:1035-1040) andtranscription factors effective in mitigating the negative effects offreezing, high salinity, and drought on plants, as well as conferringother positive effects on plant phenotype; US2004/0148654 and WO01/36596where abscisic acid is altered in plants resulting in improved plantphenotype such as increased yield and/or increased tolerance to abioticstress; WO00/006341, WO04/090143, U.S. Pat. Nos. 7,531,723, and6,992,237 where cytokinin expression is modified resulting in plantswith increased stress tolerance, such as drought tolerance, and/orincreased yield. Also see WO02/02776, WO03/052063, JP2002281975, U.S.Pat. No. 6,084,153, WO01/64898, U.S. Pat. Nos. 6,177,275, and 6,107,547(enhancement of nitrogen utilization and altered nitrogenresponsiveness). For ethylene alteration, see US2004/0128719,US2003/0166197, and WO00/32761. For plant transcription factors ortranscriptional regulators of abiotic stress, see e.g. US2004/0098764 orUS2004/0078852.

Other genes and transcription factors that affect plant growth andagronomic traits such as yield, flowering, plant growth, and/or plantstructure, can be introduced or introgressed into plants, see e.g.,WO97/49811 (LHY), WO98/56918 (ESD4), WO97/10339, and U.S. Pat. No.6,573,430 (TFL), U.S. Pat. No. 6,713,663 (FT), WO96/14414 (CON),WO96/38560, WO01/21822 (VRN1), WO00/44918 (VRN2), WO99/49064 (GI),WO00/46358 (FRI), WO97/29123, U.S. Pat. No. 6,794,560, U.S. Pat. No.6,307,126 (GAI), WO99/09174 (D8 and Rht), and WO04/076638 andWO04/031349 (transcription factors).

Development of Soybean Sublines

Sublines of 5PYPS54 may also be developed and are provided. Although5PYPS54 contains substantially fixed genetics and is phenotypicallyuniform with no off-types expected, there still remains a smallproportion of segregating loci either within individuals or within thepopulation as a whole. Sublining provides the ability to select forthese loci, which have no apparent morphological or phenotypic effect onthe plant characteristics, but may have an effect on overall yield. Forexample, the methods described in U.S. Pat. Nos. 5,437,697, 7,973,212,and US2011/0258733, and US2011/0283425 may be utilized by a breeder ofordinary skill in the art to identify genetic loci that are associatedwith yield potential to further purify the variety in order to increaseits yield. A breeder of ordinary skill in the art may fix agronomicallyrelevant loci by making them homozygous in order to optimize theperformance of the variety. The development of soybean sublines and theuse of accelerated yield technology is a plant breeding technique.

Soybean varieties such as 5PYPS54 are typically developed for use inseed and grain production. However, soybean varieties such as 5PYPS54also provide a source of breeding material that may be used to developnew soybean varieties. Plant breeding techniques known in the art andused in a soybean plant breeding program include, but are not limitedto, recurrent selection, mass selection, bulk selection, backcrossing,pedigree breeding, open pollination breeding, restriction fragmentlength polymorphism enhanced selection, genetic marker enhancedselection, making double haploids, and transformation. Oftencombinations of these techniques are used. The development of soybeanvarieties in a plant breeding program requires, in general, thedevelopment and evaluation of homozygous varieties. There are manyanalytical methods available to evaluate a new variety. The oldest andmost traditional method of analysis is the observation of phenotypictraits but genotypic analysis may also be used.

Methods for producing a soybean plant by crossing a first parent soybeanplant with a second parent soybean plant wherein the first and/or secondparent soybean plant is variety 5PYPS54 are provided. Also provided aremethods for producing a soybean plant having substantially all of themorphological and physiological characteristics of variety 5PYPS54, bycrossing a first parent soybean plant with a second parent soybean plantwherein the first and/or the second parent soybean plant is a planthaving substantially all of the morphological and physiologicalcharacteristics of variety 5PYPS54 set forth in Table 1, as determinedat the 5% significance level when grown in the same environmentalconditions. The other parent may be any soybean plant, such as a soybeanplant that is part of a synthetic or natural population. Any suchmethods using soybean variety 5PYPS54 include but are not limited toselfing, sibbing, backcrossing, mass selection, pedigree breeding, bulkselection, hybrid production, crossing to populations, and the like.These methods are well known in the art and some of the more commonlyused breeding methods are described below.

Pedigree breeding starts with the crossing of two genotypes, such as5PYPS54 or a soybean variety having all of the morphological andphysiological characteristics of 5PYPS54, and another soybean varietyhaving one or more desirable characteristics that is lacking or whichcomplements 5PYPS54. If the two original parents do not provide all thedesired characteristics, other sources can be included in the breedingpopulation. In the pedigree method, superior plants are selfed andselected in successive filial generations. In the succeeding filialgenerations, the heterozygous allele condition gives way to thehomozygous allele condition as a result of inbreeding. Typically in thepedigree method of breeding, five or more successive filial generationsof selfing and selection are practiced: e.g., F1→F2; F2→F3; F3→F4;F4→F5; etc. In some examples, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or moregenerations of selfing and selection are practiced. After a sufficientamount of inbreeding, successive filial generations will serve toincrease seed of the developed variety. Typically, the developed varietycomprises homozygous alleles at about 95% or more of its loci.

In addition to being used to create backcross conversion populations,backcrossing can also be used in combination with pedigree breeding. Asdiscussed previously, backcrossing can be used to transfer one or morespecifically desirable traits from one variety (the donor parent) to adeveloped variety (the recurrent parent), which has good overallagronomic characteristics yet may lack one or more other desirabletraits. However, the same procedure can be used to move the progenytoward the genotype of the recurrent parent but at the same time retainmany components of the non-recurrent parent by stopping the backcrossingat an early stage and proceeding with selfing and selection. Forexample, a soybean variety may be crossed with another variety toproduce a first generation progeny plant. The first generation progenyplant may then be backcrossed to one of its parent varieties to create aBC1F1. Progeny are selfed and selected so that the newly developedvariety has many of the attributes of the recurrent parent and yetseveral of the desired attributes of the donor parent. This approachleverages the value and strengths of both parents for use in new soybeanvarieties.

Therefore, in some examples a method of making a backcross conversion ofsoybean variety 5PYPS54, comprising the steps of crossing a plant ofsoybean variety 5PYPS54 or a soybean variety having all of themorphological and physiological characteristics of 5PYPS54 with a donorplant possessing a desired trait to introduce the desired trait,selecting an F1 progeny plant containing the desired trait, andbackcrossing the selected F1 progeny plant to a plant of soybean variety5PYPS54 are provided. This method may further comprise the step ofobtaining a molecular marker profile of soybean variety 5PYPS54 andusing the molecular marker profile to select for a progeny plant withthe desired trait and the molecular marker profile of 5PYPS54. Themolecular marker profile can comprise information from one or moremarkers. In one example the desired trait is a mutant gene or transgenepresent in the donor parent. In another example, the desired trait is anative trait in the donor parent.

Recurrent selection is a method used in a plant breeding program toimprove a population of plants. Variety 5PYPS54, and/or a soybeanvariety having all of the morphological and physiologicalcharacteristics of 5PYPS54, is suitable for use in a recurrent selectionprogram. The method entails individual plants cross pollinating witheach other to form progeny. The progeny are grown and the superiorprogeny selected by any number of selection methods, which includeindividual plant, half-sib progeny, full-sib progeny, and selfedprogeny. The selected progeny are cross pollinated with each other toform progeny for another population. This population is planted and,again, superior plants are selected to cross pollinate with each other.Recurrent selection is a cyclical process and therefore can be repeatedas many times as desired. The objective of recurrent selection is toimprove the traits of a population. The improved population can then beused as a source of breeding material to obtain new varieties forcommercial or breeding use, including the production of a syntheticcultivar. A synthetic cultivar is the resultant progeny formed by theintercrossing of several selected varieties.

Mass selection is a useful technique when used in conjunction withmolecular marker enhanced selection. In mass selection, seeds fromindividuals are selected based on phenotype or genotype. These selectedseeds are then bulked and used to grow the next generation. Bulkselection requires growing a population of plants in a bulk plot,allowing the plants to self-pollinate, harvesting the seed in bulk, andthen using a sample of the seed harvested in bulk to plant the nextgeneration. Also, instead of self pollination, directed pollinationcould be used as part of the breeding program.

Mutation breeding is another method of introducing new traits intosoybean variety 5PYPS54 or a soybean variety having all of themorphological and physiological characteristics of 5PYPS54. Mutationsthat occur spontaneously or that are artificially induced can be usefulsources of variability for a plant breeder. The goal of artificialmutagenesis is to increase the rate of mutation for a desiredcharacteristic. Mutation rates can be increased by many different meansincluding temperature, long-term seed storage, tissue cultureconditions, radiation; such as X-rays, gamma rays (e.g., cobalt 60 orcesium 137), neutrons, (product of nuclear fission by uranium 235 in anatomic reactor), beta radiation (emitted from radioisotopes such asphosphorus 32 or carbon 14), ultraviolet radiation (preferably from 2500to 2900 nm), or chemical mutagens such as base analogues(5-bromo-uracil), related compounds (8-ethoxy caffeine), antibiotics(streptonigrin), alkylating agents (sulfur mustards, nitrogen mustards,epoxides, ethylenamines, sulfates, sulfonates, sulfones, lactones),azide, hydroxylamine, nitrous acid, or acridines. Once a desired traitis observed through mutagenesis, the trait may then be incorporated intoexisting germplasm by traditional breeding techniques. Details ofmutation breeding can be found in “Principles of Cultivar Development”Fehr, 1993, Macmillan Publishing Company. In addition, mutations createdin other soybean plants may be used to produce a backcross conversion of5PYPS54 that comprises such mutation.

Molecular markers, which include markers identified through the use oftechniques such as isozyme electrophoresis, restriction fragment lengthpolymorphisms (RFLPs), randomly amplified polymorphic DNAs (RAPDs),arbitrarily primed polymerase chain reaction (AP-PCR), DNA amplificationfingerprinting (DAF), sequence characterized amplified regions (SCARs),amplified fragment length polymorphisms (AFLPs), simple sequence repeats(SSRs), single nucleotide polymorphisms (SNPs), and sequencing may beused in plant breeding methods utilizing 5PYPS54.

Isozyme electrophoresis and RFLPs have been widely used to determinegenetic composition. Shoemaker & Olsen (“Molecular Linkage Map ofSoybean (Glycine max L. Merr.)”, p. 6.131-6.138, in S. J. O'Brien (ed.)Genetic Maps: Locus Maps of Complex Genomes. (1993) Cold Spring HarborLaboratory Press. Cold Spring Harbor, N.Y.), developed a moleculargenetic linkage map that consisted of 25 linkage groups with about 365RFLP, 11 RAPD (random amplified polymorphic DNA), three classicalmarkers, and four isozyme loci. See also, Shoemaker “RFLP Map ofSoybean” pp 299-309 (1994), in R. L. Phillips and I. K. Vasil (ed.)describing DNA-based markers in plants. Kluwer Academic Press Dordrecht,the Netherlands.

SSR technology is an efficient and practical marker technology; moremarker loci can be routinely used and more alleles per marker locus canbe found using SSRs in comparison to RFLPs. For example, Diwan andCregan, described highly polymorphic microsatellite loci in soybean withas many as 26 alleles (Diwan and Cregan (1997) Theor Appl Genet95:220-225). Single nucleotide polymorphisms (SNPs) may also be used toidentify the unique genetic composition of 5PYPS54 and progeny varietiesretaining or derived from that unique genetic composition. Variousmolecular marker techniques may be used in combination to enhanceoverall resolution.

Soybean DNA molecular marker linkage maps have been rapidly constructedand widely implemented in genetic studies. One such study is describedin Cregan et al. (1999) Crop Sci 39:1464-1490. Sequences and PCRconditions of SSR loci in soybean, as well as the most current geneticmap, may be found in the Soybase database available online.

One use of molecular markers is quantitative trait loci (QTL) mapping.QTL mapping is the use of markers which are known to be closely linkedto alleles that have measurable effects on a quantitative trait.Selection in the breeding process is based upon the accumulation ofmarkers linked to the positive effecting alleles and/or the eliminationof the markers linked to the negative effecting alleles from the plantgenome.

Molecular markers can also be used during the breeding process for theselection of qualitative traits. For example, markers closely linked toalleles or markers containing sequences within the actual alleles ofinterest can be used to select plants that contain the alleles ofinterest during a backcrossing breeding program. The markers can also beused to select for the genome of the recurrent parent and against thegenome of the donor parent. Using this procedure can minimize the amountof genome from the donor parent that remains in the selected plants. Itcan also be used to reduce the number of crosses back to the recurrentparent needed in a backcrossing program. The use of molecular markers inthe selection process is often called genetic marker enhanced selection.

Production of Double Haploids

The production of double haploids can also be used for the developmentof plants with a homozygous phenotype in the breeding program. Forexample, a soybean plant for which variety 5PYPS54 or a soybean varietyhaving all of the phenotypic, morphological and/or physiologicalcharacteristics of 5PYPS54 is a parent can be used to produce doublehaploid plants. Double haploids are produced by the doubling of a set ofchromosomes (1 N) from a heterozygous plant to produce a completelyhomozygous individual. For example, see US Patent Publication No.2003/0005479. This can be advantageous because the process omits thegenerations of selfing needed to obtain a homozygous plant from aheterozygous source. Double haploid technology in soybean is discussedin Croser et al. (2006) Crit Rev Plant Sci 25:139-157; and Rodrigues etal. (2006) Brazilian Arc Biol Tech 49:537-545.

In some examples a process for making a substantially homozygous 5PYPS54progeny plant by producing or obtaining a seed from the cross of 5PYPS54and another soybean plant and applying double haploid methods to the F1seed or F1 plant or to any successive filial generation is provided.Based on studies in maize, and currently being conducted in soybean,such methods would decrease the number of generations required toproduce a variety with similar genetics or characteristics to 5PYPS54.See Bernardo & Kahler (2001) Theor Appl Genet 102:986-992.

In particular, a process of making seed retaining the molecular markerprofile of soybean variety 5PYPS54 is contemplated, such processcomprising obtaining or producing F1 seed for which soybean variety5PYPS54 is a parent, inducing doubled haploids to create progeny withoutthe occurrence of meiotic segregation, obtaining the molecular markerprofile of soybean variety 5PYPS54, and selecting progeny that retainthe molecular marker profile of 5PYPS54.

Methods using seeds, plants, cells, or plant parts of variety 5PYPS54 intissue culture are provided, as are the cultures, plants, parts, cells,and/or seeds derived therefrom. Tissue culture of various tissues ofsoybeans and regeneration of plants therefrom is well known and widelypublished. For example, see Komatsuda et al. (1991) Crop Sci 31:333-337;Stephens et al. “Agronomic Evaluation of Tissue-Culture-Derived SoybeanPlants” (1991) Theor Appl Genet 82:633-635; Komatsuda et al. “Maturationand Germination of Somatic Embryos as Affected by Sucrose and PlantGrowth Regulators in Soybeans Glycine gracilis Skvortz and Glycine max(L.) Merr.” (1992) Plant Cell Tissue and Organ Culture 28:103-113; Dhiret al. “Regeneration of Fertile Plants from Protoplasts of Soybean(Glycine max L. Merr.): Genotypic Differences in Culture Response”(1992) Plant Cell Rep 11:285-289; Pandey et al. “Plant Regeneration fromLeaf and Hypocotyl Explants of Glycine wightii (W. and A.) VERDC. var.longicauda” (1992) Japan J Breed 42:1-5; and Shetty et al. “Stimulationof in Vitro Shoot Organogenesis in Glycine max (Merrill.) by Allantoinand Amides” (1992) Plant Sci 81:245-251; U.S. Pat. Nos. 5,024,944 and5,008,200. Thus, another aspect is to provide cells which upon growthand differentiation produce soybean plants having the physiological andmorphological characteristics of soybean variety 5PYPS54.

Soybean seeds, plants, and plant parts of variety 5PYPS54 may be cleanedand/or treated. Provided are methods for producing treated seedcomprising treating a seed described herein. Provided are methods forproducing cleaned seed comprising cleaning a seed or a population orplurality of seeds described herein. The resulting seeds, plants, orplant parts produced by the cleaning and/or treating process(es) mayexhibit enhanced yield characteristics. Enhanced yield characteristicscan include one or more of the following: increased germinationefficiency under normal and/or stress conditions, improved plantphysiology, growth and/or development, such as water use efficiency,water retention efficiency, improved nitrogen use, enhanced carbonassimilation, improved photosynthesis, and accelerated maturation, andimproved disease and/or pathogen tolerance. Yield characteristics canfurthermore include enhanced plant architecture (under stress andnon-stress conditions), including but not limited to early flowering,flowering control for hybrid seed production, seedling vigor, plantsize, internode number and distance, root growth, seed size, fruit size,pod size, pod or ear number, seed number per pod or ear, seed mass,enhanced seed filling, reduced seed dispersal, reduced pod dehiscenceand lodging resistance. Further yield characteristics include seedcomposition, such as carbohydrate content, protein content, oil contentand composition, nutritional value, reduction in anti-nutritionalcompounds, improved processability, and better storage stability.

Cleaning a seed or seed cleaning refers to the removal of impurities anddebris material from the harvested seed. Material to be removed from theseed includes but is not limited to soil, and plant waste, chaff,pebbles, weed seeds, broken soybean seeds, fungi, bacteria, insectmaterial, including insect eggs, larvae, and parts thereof, and anyother pests that exist with the harvested crop. The terms cleaning aseed or seed cleaning also refer to the removal of any debris orimpurities such as low quality, infested, or infected seeds and seeds ofdifferent species that are foreign to the sample.

Treating a seed or applying a treatment to a seed refers to theapplication of a composition to a seed as a coating or otherwise. Themethod can include a step of contacting the seed with a composition tocoat the surface of the seed or to adhere the composition to the seed.The composition may be applied to the seed in a seed treatment at anytime from harvesting of the seed to sowing of the seed. The compositionmay be applied using methods including but not limited to mixing in acontainer, mechanical application, tumbling, spraying, misting, andimmersion. Thus, the composition may be applied as a powder, acrystalline, a ready-to-use, a slurry, a mist, and/or a soak. For ageneral discussion of techniques used to apply fungicides to seeds, see“Seed Treatment,” 2d ed., (1986), edited by K. A Jeffs (chapter 9). Thecomposition to be used as a seed treatment can comprise one or more of apesticide, a fungicide, an insecticide, a nematicide, an antimicrobial,an inoculant, a growth promoter, a polymer, a flow agent, a coating, orany combination thereof. General classes or family of seed treatmentagents include triazoles, anilides, pyrazoles, carboxamides, succinatedehydrogenase inhibitors (SDHI), triazolinthiones, strobilurins, amides,and anthranilic diamides. In some examples, the seed treatment comprisestrifloxystrobin, azoxystrobin, metalaxyl, metalaxyl-m, mefenoxam,fludioxinil, imidacloprid, thiamethoxam, thiabendazole, ipconazole,penflufen, sedaxane, prothioconazole, picoxystrobin, penthiopyrad,pyraclastrobin, xemium, Rhizobia spp., Bradyrhizobium spp. (e.g., B.japonicum), Bacillus spp. (e.g., B. firmus, B. pumilus, B. subtilis),lipo-chitooligosaccharide, clothianidin, cyazapyr, rynaxapyr, abamectin,and any combination thereof. In some examples the seed treatmentcomprises trifloxystrobin, metalaxyl, imidacloprid, Bacillus spp., andany combination thereof. In some examples the seed treatment comprisespicoxystrobin, penthiopyrad, cyazapyr, ranaxapyr, and any combinationthereof. In some examples, the seed treatment improves seed germinationunder normal and/or stress environments, early stand count, vigor,yield, root formation, nodulation, and any combination thereof. In someexamples seed treatment reduces seed dust levels, insect damage,pathogen establishment and/or damage, plant virus infection and/ordamage, and any combination thereof.

Soybean seeds, plants, and plant parts of variety 5PYPS54 may be used orprocessed for food, animal feed, or a raw material(s) for industry.Seeds from variety 5PYPS54 can be crushed, or a component of the seedscan be extracted in order to make a plant product, such as proteinconcentrate, protein isolate, soybean hulls, meal, flour, or oil for afood or feed product. Methods of producing a plant product or acommodity product, such as protein concentrate, protein isolate, soybeanhulls, meal, flour, or oil for a food or feed product by processing theplants, plant parts or grain disclosed herein are provided. Alsoprovided are the protein concentrate, protein isolate, soybean hulls,meal, flour, or oil produced by the methods.

Soybean is also used as a food source for both animals and humans.Soybean is widely used as a source of protein for animal feeds forpoultry, swine, and cattle, or specialty pet foods. For humanconsumption soybean meal is made into soybean flour which is processedto protein concentrates used for meat extenders. Production of edibleprotein ingredients from soybean offers a healthy, less expensivereplacement for animal protein in meats and dairy products. Duringprocessing of whole soybeans, the fibrous hull is removed and the oil isextracted. The remaining soybean meal is a combination of carbohydratesand approximately 50% protein.

Oil extracted from soybeans is used for cooking oil, margarine, andsalad dressings. Soybean oil has a typical composition of 11% palmitic,4% stearic, 25% oleic, 50% linoleic, and 9% linolenic fatty acidcontent. Fatty acid composition can be altered, for example, throughtransformation, breeding or a combination thereof, for improvedoxidative stability and nutrition. For example, oleic acid can be raisedto at least 70% or 75% of the total fatty acid content, and linolenicacid can be reduced to less than 5% or 3% of the total fatty acidcontent. Oil with 3% or less linolenic acid is classified as lowlinolenic oil, oil with less than 1% linolenic acid is classified asultra-low linolenic oil. Oil with 70% or higher of oleic acid isclassified as high oleic oil.

Industrial uses of soybean oil, which is typically subjected to furtherprocessing, include ingredients for paints, plastics, fibers,detergents, cosmetics, lubricants, and biodiesel fuel. Soybean oil maybe split, inter-esterified, sulfurized, epoxidized, polymerized,ethoxylated, or cleaved. To produce oil, the harvested soybeans arecracked, adjusted for moisture content, rolled into flakes, and then theoil is solvent-extracted. The oil extract is refined, optionally blendedand/or hydrogenated. The mixture of triglycerides can be split andseparated into pure fatty acids, which can be combined withpetroleum-derived alcohols or acids, nitrogen, sulfonates, chlorine, orwith fatty alcohols derived from fats and oils.

Soybeans are also used as a food source for both animals and humans.Soybeans are widely used as a source of protein for animal feed. Thefibrous hull is removed from whole soybean and the oil is extracted. Theremaining meal is a combination of carbohydrates and approximately 50%protein. This remaining meal is heat treated under well-establishedconditions and ground in a hammer mill. Soybean is a predominant sourcefor livestock feed components.

In addition to soybean meal, soybean can be used to produce soy flour.Soy flour refers to defatted soybeans where special care was takenduring desolventizing to minimize protein denaturation and to retain ahigh nitrogen solubility index (NSI) in making the flour. Soy flour isthe typical starting material for production of soy concentrate and soyprotein isolate. Defatted soy flour is obtained from solvent extractedflakes, and contains less than 1% oil. Full-fat soy flour is made fromwhole beans and contains about 18% to 20% oil. Low-fat soy flour is madeby adding back some oil to defatted soy flour. The lipid content varies,but is usually between 4.5-9%. High-fat soy flour can also be producedby adding soybean oil to defatted flour at the level of 15%.Lecithinated soy flour is made by adding soybean lecithin to defatted,low-fat or high-fat soy flours to increase dispersibility and impartemulsifying properties.

For human consumption, soybean can be used to produce edible ingredientswhich serve as an alternative source of dietary protein. Common examplesinclude milk, cheese, and meat substitutes. Additionally, soybean can beused to produce various types of fillers for meat and poultry products.Vitamins and/or minerals may be added to make soy products nutritionallymore equivalent to animal protein sources as the protein quality isalready roughly equivalent.

All publications, patents, and patent applications mentioned in thespecification are indicative of the level of those skilled in the art towhich this invention pertains. All such publications, patents, andpatent applications are incorporated by reference herein for the purposecited to the same extent as if each was specifically and individuallyindicated to be incorporated by reference herein.

The foregoing invention has been described in detail by way ofillustration and example for purposes of clarity and understanding. Asis readily apparent to one skilled in the art, the foregoing are onlysome of the methods and compositions that illustrate the embodiments ofthe foregoing invention. It will be apparent to those of ordinary skillin the art that variations, changes, modifications, and alterations maybe applied to the compositions and/or methods described herein withoutdeparting from the true spirit, concept, and scope of the invention.

As used herein, the terms “comprises,” “comprising,” “includes,”“including,” “has,” “having,” “contains”, “containing,” “characterizedby” or any other variation thereof, are intended to cover anon-exclusive inclusion. For example, a composition, mixture, process,method, article, or apparatus that comprises a list of elements is notnecessarily limited to only those elements but may include otherelements not expressly listed or inherent to such composition, mixture,process, method, article, or apparatus. The transitional phrase“consisting of” excludes any element, step, or ingredient other thanthose recited except for impurities ordinarily associated therewith.When the phrase “consisting of” appears in a clause of the body of aclaim, rather than immediately following the preamble, it limits onlythe element set forth in that clause; other elements are not excludedfrom the claim as a whole. The transitional phrase “consistingessentially of” is used to define a composition, method or apparatusthat includes materials, steps, features, components, or elements, inaddition to those literally disclosed, provided that these additionalmaterials, steps, features, components, or elements do not materiallyaffect the basic characteristic(s).

Unless expressly stated to the contrary, “or” is used as an inclusiveterm. For example, a condition A or B is satisfied by any one of thefollowing: A is true (or present) and B is false (or not present), A isfalse (or not present) and B is true (or present), and both A and B aretrue (or present). The indefinite articles “a” and “an” preceding anelement or component are nonrestrictive regarding the number ofinstances (i.e., occurrences) of the element or component. Therefore “a”or “an” should be read to include one or at least one, and the singularword form of the element or component also includes the plural unlessthe number is obviously meant to be singular.

DEPOSITS

Applicant has made a deposit of seeds of Soybean Variety 5PYPS54 withthe American Type Culture Collection (ATCC), 10801 University Boulevard,Manassas, Va. 20110 USA, as ATCC Deposit No. PTA-126069. The seedsdeposited with the ATCC on Aug. 9, 2019 were taken from the seed stockmaintained by Pioneer Hi-Bred International, Inc., 7250 NW 62^(nd)Avenue, Johnston, Iowa 50131 since prior to the filing date of thisapplication. Access to this seed stock will be available during thependency of the application to the Commissioner of Patents andTrademarks and persons determined by the Commissioner to be entitledthereto upon request. Upon allowance of any claims in the application,the Applicant will make the deposit available to the public pursuant to37 C.F.R. § 1.808. This deposit of Soybean Variety 5PYPS54 will bemaintained in the ATCC depository, which is a public depository, for aperiod of 30 years, or 5 years after the most recent request, or for theenforceable life of the patent, whichever is longer, and will bereplaced if it becomes nonviable during that period. Additionally,Applicant has or will satisfy all the requirements of 37 C.F.R. §§1.801-1.809, including providing an indication of the viability of thesample upon deposit. Applicant has no authority to waive anyrestrictions imposed by law on the transfer of biological material orits transportation in commerce. Applicant does not waive anyinfringement of their rights granted under this patent or under thePlant Variety Protection Act (7 USC 2321 et seq.).

Soybean Variety 5PYPS54

Soybean variety 5PYPS54 has shown uniformity and stability for alltraits, as described in the following variety description information.Soybean variety 5PYPS54 was developed from a cross of 5PRNY93 with aversion of XB38AT13 comprising glyphosate and dicamba resistance.Variety 5PYPS54 was developed using the method described in Table 2. Ithas been self-pollinated a sufficient number of generations, withcareful attention to uniformity of plant type to ensure a sufficientlevel of homozygosity and phenotypic stability. The variety has beenincreased with continued observation for uniformity. No variant traitshave been observed or are expected.

TABLE 1 Variety Description Information Variety Name 5PYPS54 RelativeMaturity 3.5 Average Yield per Acre 63.1 Harvest Standability 6 FieldEmergence 77 Herbicide Resistance Glyphosate, dicamba & sulfonylureaGrams per Hundred Seeds 15.8 Phytophthora Resistance Gene NonePhytophthora Field Tolerance 3 Iron-deficiency Chlorosis 4 Downy Mildew66 White Mold Tolerance 33 Cyst Nematode Race 3 9 Cyst Nematode Race 149 Sudden Death Syndrome 5 Charcoal Rot 4 Brown Stem Rot 99 Frogeye LeafSpot 4 Cercospora Tolerance Canopy Width 5 Height/Maturity 5 PlantGrowth Habit Ind % Protein @ 13% H20 33.9 % Oil @ 13% H2O 20 Seed SizeScore 6 Seed Size Range 2750-3150 Shattering 77 Flower Color WPubescence Color G Hila Color BF Pod Color BR Seed Coat Luster D SeedShape E Seed Protein Peroxidase Activity Mixed Hypocotyl Color G LeafColor Score 5 Leaf Shape OVT

TABLE 2 BREEDING HISTORY FOR 5PYPS54 Year Detail of Stage 2015Bi-parental cross 2015 F1 growout harvested in bulk 2015 F2 single plantselections made 2016 Purification - individual plant row harvested andadvanced 2016 Purification - individual plant row harvested and advanced2016 Regional area yield testing 2016 Foundation seed production 2017Seed stock and production seed 2017 Elite wide-area yield testing

What is claimed:
 1. A plant or a seed of soybean variety 5PYPS54,representative seed of the variety having been deposited under ATCCAccession Number PTA-126069.
 2. A soybean plant, or part thereof,produced by growing the seed of claim
 1. 3. A method for producingtreated seed, the method comprising applying a seed treatment to theseed of claim
 1. 4. A soybean seed obtained by introducing a transgeneinto the plant or seed of claim 1, wherein the soybean seed produces asoybean plant comprising the transgene and otherwise comprising all thephysiological and morphological characteristics of soybean variety5PYPS54 when grown under the same environmental conditions.
 5. The seedof claim 4, wherein the transgene confers a trait selected from thegroup consisting of male sterility, a site-specific recombination site,abiotic stress tolerance, altered phosphate, altered antioxidants,altered fatty acids, altered essential amino acids, alteredcarbohydrates, herbicide resistance, insect resistance, and diseaseresistance.
 6. A soybean plant produced by growing the seed of claim 4.7. A method for producing treated seed, the method comprising applying aseed treatment to the seed of claim
 4. 8. A method for producing soybeanseed, the method comprising harvesting soybean seed from a cross of twosoybean plants, wherein at least one soybean plant is the soybean plantof claim
 1. 9. An F1 soybean seed produced by the method of claim
 8. 10.A method for developing a second soybean plant, the method comprisingapplying plant breeding techniques to a plant grown from the seed ofclaim 9, wherein application of the techniques results in development ofthe second soybean plant.
 11. A method comprising isolating nucleicacids from the plant or seed of claim
 1. 12. A method of producing asoybean plant comprising a locus conversion, the method comprisingintroducing a locus conversion into the plant of claim 1, wherein thelocus conversion confers a trait selected from the group consisting ofmale sterility, a site-specific recombination site, abiotic stresstolerance, altered phosphate, altered antioxidants, altered fatty acids,altered essential amino acids, altered carbohydrates, herbicideresistance, insect resistance, and disease resistance.
 13. A soybeanplant produced by the method of claim 12, wherein the soybean plantcomprises the locus conversion and otherwise comprises essentially allof the physiological and morphological characteristics of soybeanvariety 5PYPS54 when grown under the same environmental conditions. 14.The soybean plant of claim 13, wherein the locus conversion comprises atransgene encoding a Bacillus thuringiensis (Bt) endotoxin.
 15. Thesoybean plant of claim 13, wherein the locus conversion is introduced bybackcrossing or transformation.
 16. A soybean commodity plant productproduced from the plant or seed of claim 1, wherein the commodity plantproduct comprises at least one cell of soybean variety 5PYPS54.
 17. Asoybean plant expressing all the physiological and morphologicalcharacteristics of the soybean plant of claim 2, representative seed ofthe variety having been deposited under ATCC Accession Number 126069.18. A seed, plant, plant part, or plant cell of soybean variety 5PYPS54,representative seed of the soybean variety 5PYPS54 having been depositedunder ATCC Accession Number 126069, wherein the seed, plant, plant partor plant cell of soybean variety 5PYPS54 further comprises a singlelocus conversion.
 19. A method for producing treated seed, the methodcomprising applying a seed treatment to the converted seed of claim 18.20. A soybean commodity plant product produced from the plant or seed ofclaim 18, wherein the commodity plant product comprises at least onecell of the plant or seed.